Long list of modified files

Hi, installed the Verification Tool on a local install of Joomla version 1.5.15. I ran the tool and it comes back with a list of I am guessing all the Joomla files, saying they are all modified. I did an Exam Dif on the first file in the list with a copy of the file from a full file set of the 1.5.15 install and the files came up as exactly the same.

I ran the Tool a couple of times with the same results, then logged out , logged back in and tried again with the same results.
The check was set to 1.5.15.xml the parameters were set to Find Version "No" Memory Limit "256 MB" Max Execute "600"

Here is a look at my local Wampserver

Diagnostic Information
Joomla! Version: Joomla! 1.5.15 Stable [ Wojmamni Ama Mamni ] 05-November-2009 04:00 GMT
configuration.php: Writable (Mode: 666 ) | RG_EMULATION: N/A
Architecture/Platform: Windows NT 5.1 ( i586) | Web Server: Apache/2.2.8 (Win32) PHP/5.2.9 ( xxxxxx ) | PHP Version: 5.2.9
PHP Requirements: register_globals: Disabled | magic_quotes_gpc: Disabled | safe_mode: Disabled | MySQL Support: Yes | XML Support: Yes | zlib Support: Yes
mbstring Support (1.5): Yes | iconv Support (1.5): Yes | save.session_path: Writable | Max.Execution Time: 30 seconds | File Uploads: Enabled
MySQL Version: 5.0.51b-community-nt ( 127.0.0.1 via TCP/IP )

Extended Information:
SEF: Enabled (without ReWrite) | FTP Layer: Disabled | htaccess: Not Implemented
PHP/suExec: User and Web Server accounts are not the same. (PHP/suExec probably not installed)
PHP Environment: API: apache2handler | MySQLi: Yes | Max. Memory: 128M | Max. Upload Size: 2M | Max. Post Size: 8M | Max. Input Time: 60 | Zend Version: 2.2.0
Disabled Functions:
MySQL Client: 5.0.51a ( latin1 )

More info;
the modified files are all .xml and .html files so it is not all the Joomla files it is incorrectly showing as modified. I also installed the Verification Tool on another site on my local Wampserver, this one in the root www folder and the Tool worked fine. The site where it is having problems is in a subfolder of the www root folder.

More Info;
I checked the MD5 sum in your 1.5.15xml file against the sum for one of my files marked as modified
File on Wampserver administrator/components/com_banners/banners.xml--f21e502539c4603fda94e986e83f9875
File from 1.5.15 zip

---

253a96a169b5ef87a72aa8077a1d10d9
File from 1.5.10 zip

---

253a96a169b5ef87a72aa8077a1d10d9
Check sum from your 1.5.15.xml file

---

253a96a169b5ef87a72aa8077a1d10d9

When I open all three files in ExamDiff its says they are exactly the same. I checked properties for creation dates and modified dates, they are different for all three files but the sizes are all the same.

The WampServer site in question was created from a JoomlaPack backup of a live site. It seems that JoomlaPack does something to the .xml and .html files during backup that changes their MD5 check sum.

OK I just installed the Verification Tool on my live site, it is still in version 1.5.14 of Joomla. It has produced an even larger list of files that do not match the MD5 check sum. The problem does not seem to be with JoomlaPack then but is a problem on the live server. Does anyone know what could have caused so many files to no longer have the correct check sum?

Here is the list it produced on the live site, only a few of these files have actually been modified by me, again it is mostly .xml and .html files. I see a lot of TinyMCE files listed, could that be because I have JCE installed and it may have modified those files?

Modified Files

* /var/www/html/administrator/components/com_banners/banners.xml
* /var/www/html/administrator/components/com_banners/config.xml
* /var/www/html/administrator/components/com_cache/cache.xml
* /var/www/html/administrator/components/com_config/config.xml
* /var/www/html/administrator/components/com_contact/config.xml
* /var/www/html/administrator/components/com_contact/contact.xml
* /var/www/html/administrator/components/com_contact/contact_items.xml
* /var/www/html/administrator/components/com_content/content.xml
* /var/www/html/administrator/components/com_content/models/article.xml
* /var/www/html/administrator/components/com_cpanel/cpanel.xml
* /var/www/html/administrator/components/com_frontpage/frontpage.xml
* /var/www/html/administrator/components/com_installer/installer.xml
* /var/www/html/administrator/components/com_languages/languages.xml
* /var/www/html/administrator/components/com_massmail/config.xml
* /var/www/html/administrator/components/com_massmail/massmail.xml
* /var/www/html/administrator/components/com_media/media.xml
* /var/www/html/administrator/components/com_menus/config.xml
* /var/www/html/administrator/components/com_menus/menus.xml
* /var/www/html/administrator/components/com_menus/models/metadata/component.xml
* /var/www/html/administrator/components/com_menus/models/metadata/menulink.xml
* /var/www/html/administrator/components/com_menus/models/metadata/separator.xml
* /var/www/html/administrator/components/com_menus/models/metadata/url.xml
* /var/www/html/administrator/components/com_messages/messages.xml
* /var/www/html/administrator/components/com_modules/modules.xml
* /var/www/html/administrator/components/com_newsfeeds/newsfeeds.xml
* /var/www/html/administrator/components/com_plugins/plugins.xml
* /var/www/html/administrator/components/com_poll/poll.xml
* /var/www/html/administrator/components/com_search/search.xml
* /var/www/html/administrator/components/com_templates/templates.xml
* /var/www/html/administrator/components/com_trash/trash.xml
* /var/www/html/administrator/components/com_users/config.xml
* /var/www/html/administrator/components/com_users/models/author.xml
* /var/www/html/administrator/components/com_users/models/registered.xml
* /var/www/html/administrator/components/com_users/models/user.xml
* /var/www/html/administrator/components/com_users/users.xml
* /var/www/html/administrator/components/com_weblinks/weblinks.xml
* /var/www/html/administrator/help/en-GB/joomla.whatsnew10.html
* /var/www/html/administrator/help/en-GB/screen.banner.categories.edit.html
* /var/www/html/administrator/help/en-GB/screen.banner.categories.html
* /var/www/html/administrator/help/en-GB/screen.banners.client.edit.html
* /var/www/html/administrator/help/en-GB/screen.banners.client.html
* /var/www/html/administrator/help/en-GB/screen.banners.edit.html
* /var/www/html/administrator/help/en-GB/screen.banners.html
* /var/www/html/administrator/help/en-GB/screen.cache.html
* /var/www/html/administrator/help/en-GB/screen.categories.edit.html
* /var/www/html/administrator/help/en-GB/screen.categories.html
* /var/www/html/administrator/help/en-GB/screen.checkin.html
* /var/www/html/administrator/help/en-GB/screen.config.html
* /var/www/html/administrator/help/en-GB/screen.contact_details.categories.edit.html
* /var/www/html/administrator/help/en-GB/screen.contact_details.categories.html
* /var/www/html/administrator/help/en-GB/screen.contactmanager.edit.html
* /var/www/html/administrator/help/en-GB/screen.contactmanager.html
* /var/www/html/administrator/help/en-GB/screen.content.categories.edit.html
* /var/www/html/administrator/help/en-GB/screen.content.categories.html
* /var/www/html/administrator/help/en-GB/screen.content.edit.html
* /var/www/html/administrator/help/en-GB/screen.content.html
* /var/www/html/administrator/help/en-GB/screen.cpanel.html
* /var/www/html/administrator/help/en-GB/screen.frontpage.html
* /var/www/html/administrator/help/en-GB/screen.installer.html
* /var/www/html/administrator/help/en-GB/screen.languages.html
* /var/www/html/administrator/help/en-GB/screen.mediamanager.html
* /var/www/html/administrator/help/en-GB/screen.menumanager.html
* /var/www/html/administrator/help/en-GB/screen.menumanager.new.html
* /var/www/html/administrator/help/en-GB/screen.menus.edit.html
* /var/www/html/administrator/help/en-GB/screen.menus.html
* /var/www/html/administrator/help/en-GB/screen.messages.edit.html
* /var/www/html/administrator/help/en-GB/screen.messages.inbox.html
* /var/www/html/administrator/help/en-GB/screen.messages.read.html
* /var/www/html/administrator/help/en-GB/screen.modules.edit.html
* /var/www/html/administrator/help/en-GB/screen.modules.html
* /var/www/html/administrator/help/en-GB/screen.modules.new.html
* /var/www/html/administrator/help/en-GB/screen.modulesadministrator.edit.html
* /var/www/html/administrator/help/en-GB/screen.modulessite.edit.html
* /var/www/html/administrator/help/en-GB/screen.newsfeeds.categories.edit.html
* /var/www/html/administrator/help/en-GB/screen.newsfeeds.categories.html
* /var/www/html/administrator/help/en-GB/screen.newsfeeds.edit.html
* /var/www/html/administrator/help/en-GB/screen.newsfeeds.html
* /var/www/html/administrator/help/en-GB/screen.plugins.edit.html
* /var/www/html/administrator/help/en-GB/screen.plugins.html
* /var/www/html/administrator/help/en-GB/screen.polls.edit.html
* /var/www/html/administrator/help/en-GB/screen.polls.html
* /var/www/html/administrator/help/en-GB/screen.sections.edit.html
* /var/www/html/administrator/help/en-GB/screen.sections.html
* /var/www/html/administrator/help/en-GB/screen.stats.searches.html
* /var/www/html/administrator/help/en-GB/screen.system.info.html
* /var/www/html/administrator/help/en-GB/screen.templates.html
* /var/www/html/administrator/help/en-GB/screen.trashmanager.html
* /var/www/html/administrator/help/en-GB/screen.users.edit.html
* /var/www/html/administrator/help/en-GB/screen.users.html
* /var/www/html/administrator/help/en-GB/screen.users.massmail.html
* /var/www/html/administrator/help/en-GB/screen.weblink.edit.html
* /var/www/html/administrator/help/en-GB/screen.weblink.html
* /var/www/html/administrator/help/en-GB/screen.weblinks.categories.edit.html
* /var/www/html/administrator/help/en-GB/screen.weblinks.categories.html
* /var/www/html/administrator/language/en-GB/en-GB.xml
* /var/www/html/administrator/modules/mod_custom/mod_custom.xml
* /var/www/html/administrator/modules/mod_footer/mod_footer.xml
* /var/www/html/administrator/modules/mod_latest/mod_latest.xml
* /var/www/html/administrator/modules/mod_logged/mod_logged.xml
* /var/www/html/administrator/modules/mod_login/mod_login.xml
* /var/www/html/administrator/modules/mod_menu/mod_menu.xml
* /var/www/html/administrator/modules/mod_online/mod_online.xml
* /var/www/html/administrator/modules/mod_popular/mod_popular.xml
* /var/www/html/administrator/modules/mod_quickicon/mod_quickicon.xml
* /var/www/html/administrator/modules/mod_stats/mod_stats.xml
* /var/www/html/administrator/modules/mod_status/mod_status.xml
* /var/www/html/administrator/modules/mod_submenu/mod_submenu.xml
* /var/www/html/administrator/modules/mod_title/mod_title.xml
* /var/www/html/administrator/modules/mod_toolbar/mod_toolbar.xml
* /var/www/html/administrator/modules/mod_unread/mod_unread.xml
* /var/www/html/administrator/templates/khepri/images/h_teal/j_header_left.png
* /var/www/html/administrator/templates/khepri/images/h_teal/j_header_right_rtl.png
* /var/www/html/administrator/templates/khepri/login.php
* /var/www/html/administrator/templates/khepri/params.ini
* /var/www/html/components/com_contact/metadata.xml
* /var/www/html/components/com_contact/views/contact/tmpl/default.xml
* /var/www/html/components/com_content/metadata.xml
* /var/www/html/components/com_content/views/archive/tmpl/default.xml
* /var/www/html/components/com_content/views/article/metadata.xml
* /var/www/html/components/com_content/views/article/tmpl/default.xml
* /var/www/html/components/com_content/views/article/tmpl/form.xml
* /var/www/html/components/com_content/views/article/tmpl/pagebreak.xml
* /var/www/html/components/com_mailto/mailto.xml
* /var/www/html/components/com_mailto/views/mailto/metadata.xml
* /var/www/html/components/com_mailto/views/sent/metadata.xml
* /var/www/html/components/com_newsfeeds/metadata.xml
* /var/www/html/components/com_poll/views/poll/metadata.xml
* /var/www/html/components/com_poll/views/poll/tmpl/default.xml
* /var/www/html/components/com_search/views/search/metadata.xml
* /var/www/html/components/com_user/user.xml
* /var/www/html/components/com_user/views/login/metadata.xml
* /var/www/html/components/com_user/views/login/tmpl/default.xml
* /var/www/html/components/com_user/views/login/tmpl/metadata.xml
* /var/www/html/components/com_user/views/register/metadata.xml
* /var/www/html/components/com_user/views/register/tmpl/default.xml
* /var/www/html/components/com_user/views/remind/metadata.xml
* /var/www/html/components/com_user/views/remind/tmpl/default.xml
* /var/www/html/components/com_user/views/reset/metadata.xml
* /var/www/html/components/com_user/views/reset/tmpl/complete.xml
* /var/www/html/components/com_user/views/reset/tmpl/confirm.xml
* /var/www/html/components/com_user/views/reset/tmpl/default.xml
* /var/www/html/components/com_user/views/user/metadata.xml
* /var/www/html/components/com_user/views/user/tmpl/form.xml
* /var/www/html/components/com_weblinks/metadata.xml
* /var/www/html/components/com_weblinks/views/categories/metadata.xml
* /var/www/html/components/com_weblinks/views/category/metadata.xml
* /var/www/html/components/com_weblinks/views/weblink/tmpl/form.xml
* /var/www/html/components/com_wrapper/metadata.xml
* /var/www/html/components/com_wrapper/views/wrapper/metadata.xml
* /var/www/html/components/com_wrapper/views/wrapper/tmpl/default.xml
* /var/www/html/components/com_wrapper/wrapper.xml
* /var/www/html/images/joomla_logo_black.jpg
* /var/www/html/language/en-GB/en-GB.xml
* /var/www/html/libraries/joomla/template/tmpl/breadcrumbs.html
* /var/www/html/libraries/phputf8/README
* /var/www/html/libraries/tcpdf/CHANGELOG.TXT
* /var/www/html/libraries/tcpdf/README.TXT
* /var/www/html/modules/mod_archive/mod_archive.xml
* /var/www/html/modules/mod_banners/mod_banners.xml
* /var/www/html/modules/mod_custom/mod_custom.xml
* /var/www/html/modules/mod_footer/mod_footer.xml
* /var/www/html/modules/mod_latestnews/mod_latestnews.xml
* /var/www/html/modules/mod_login/mod_login.xml
* /var/www/html/modules/mod_mostread/mod_mostread.xml
* /var/www/html/modules/mod_poll/mod_poll.xml
* /var/www/html/modules/mod_random_image/mod_random_image.xml
* /var/www/html/modules/mod_related_items/mod_related_items.xml
* /var/www/html/modules/mod_sections/mod_sections.xml
* /var/www/html/modules/mod_stats/mod_stats.xml
* /var/www/html/modules/mod_syndicate/mod_syndicate.xml
* /var/www/html/modules/mod_whosonline/mod_whosonline.xml
* /var/www/html/modules/mod_wrapper/mod_wrapper.xml
* /var/www/html/plugins/authentication/example.xml
* /var/www/html/plugins/authentication/gmail.xml
* /var/www/html/plugins/authentication/joomla.xml
* /var/www/html/plugins/authentication/ldap.xml
* /var/www/html/plugins/authentication/openid.xml
* /var/www/html/plugins/content/emailcloak.xml
* /var/www/html/plugins/content/example.xml
* /var/www/html/plugins/content/geshi.xml
* /var/www/html/plugins/content/loadmodule.xml
* /var/www/html/plugins/content/pagebreak.xml
* /var/www/html/plugins/content/pagenavigation.xml
* /var/www/html/plugins/content/vote.xml
* /var/www/html/plugins/editors/none.xml
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/blank.htm
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/langs/en.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/license.txt
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/_template/popup.htm
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/advhr/css/advhr.css
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/advhr/editor_plugin_src.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/advhr/js/rule.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/advhr/langs/en_dlg.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/advhr/rule.htm
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/advimage/css/advimage.css
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/advimage/editor_plugin_src.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/advimage/image.htm
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/advimage/js/image.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/advimage/langs/en_dlg.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/advlink/css/advlink.css
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/advlink/editor_plugin_src.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/advlink/js/advlink.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/advlink/langs/en_dlg.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/advlink/link.htm
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/autosave/editor_plugin_src.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/bbcode/editor_plugin_src.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/compat2x/editor_plugin_src.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/contextmenu/editor_plugin_src.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/devkit/devkit.htm
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/directionality/editor_plugin_src.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/emotions/editor_plugin_src.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/emotions/emotions.htm
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/emotions/js/emotions.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/emotions/langs/en_dlg.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/example/dialog.htm
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/example/editor_plugin_src.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/example/js/dialog.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/example/langs/en.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/example/langs/en_dlg.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/flash/flash.htm
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/fullpage/blank.htm
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/fullpage/css/fullpage.css
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/fullpage/editor_plugin_src.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/fullpage/fullpage.htm
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/fullpage/js/fullpage.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/fullpage/langs/en_dlg.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/fullscreen/editor_plugin_src.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/fullscreen/fullscreen.htm
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/iespell/editor_plugin_src.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/iespell/readme.txt
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/inlinepopups/editor_plugin_src.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/inlinepopups/template.htm
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/insertdatetime/editor_plugin_src.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/layer/editor_plugin_src.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/media/css/content.css
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/media/css/media.css
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/media/editor_plugin_src.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/media/js/embed.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/media/js/media.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/media/langs/en_dlg.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/media/media.htm
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/nonbreaking/editor_plugin_src.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/noneditable/editor_plugin_src.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/pagebreak/editor_plugin_src.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/paste/blank.htm
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/paste/editor_plugin_src.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/paste/js/pastetext.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/paste/js/pasteword.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/paste/langs/en_dlg.js
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/paste/pastetext.htm
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/paste/pasteword.htm
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/preview/example.html
* /var/www/html/plugins/editors/tinymce/jscripts/tiny_mce/plugins/preview/jscripts/embed.js
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sourcecoast wrote: Thanks for all the info.

I will try doing a JoomlaPack backup and see if I can reproduce the same issue.

It could be a difference in whitespace or newline characters that is causing the MD5 to change. Diff programs will typically ignore those kind of differences.

Let me know if you figure anything else out.

I think I have ruled out JoomlaPack as the cause. I uploaded the full file set for the latest version of Joomla, 1.5.17 and I still got a long list of .xml .htm, .html and most of the tinyMCE plugin folder.

I then thought it may be the older version of FileZilla I was using so I updated to the latest version and re-uploaded the full file set, but the long list of modified files was still there. I then thought it could be that FTP client so I uploaded a file that showed as modified with WS_FTP. The file on the server showed a smaller size then the local copy and when I uploaded the local copy the file size then showed correctly in the WS_FTP window. I then ran a verification again but the file I just uploaded again showed as modified.

I think I have ruled out FTP client as the source of the problem and JoomlaPack so now I am guessing that it is a Host filter that may be changing the MD5 check sum of the files as they are uploaded to the server. I will ask them about that and post back here when I get an answer.

I also noticed that the verification runs quicker after the first time, could it be caching results and I am seeing a cached list rather then a new list?

After two weeks we have made some progress. We have found that if the files that show as modified are uploaded in Binary mode then they do not show up as modified. My guess is that their FTP server is maybe removing white space from ASCII files. I do not believe though that uploading all files in Binary mode is the answer, I remember having problems a long time ago because ASCII files had been uploaded in Binary mode.

I tried to test this theory by downloading one of the files listed as modified
administrator/components/com_cache/cache.xml
but when I checked the hash of the downloaded file using MD5 it was the same has as the original file in the full file set I downloaded from Joomla. I then ran the Verification Tool on the site again and the file was still listed as modified. I then downloaded the 1.5.17.xml file from my site that the Verification Tool was using. I found the file in the list and the check sum listed matched the file I downloaded from the site, the same one the tool lists as modified.

It would now seem that the Tool is creating the wrong hash for the xml, html, htm, files and that one folder path of files on the site. Does the Tool have any dependencies that could be missing from my site or the Apache server config?

I just downloaded another file listed as modified and compared its hash against the one in the 1.5.17.xml list and it matches, the file is not modified. Could this be a cache problem, does Verification Tool keep a cache of the last list that it could be re-displaying? I tried a refresh of the page and a F5 of the page but still get the same files listed as modified.

OK another test, is the FTP transfer modifying the file back to its original state? I use the Hosts File Manager to download the same cache.xml file, I then compared its hash against the one in the xml list, it did not match. I compared file sizes, the one on the Host site is 503 bytes the original is 515 bytes. When I downloaded the file using teh Hoste's File Manager I got the 503 file, when I FTP'ed the file down it was 515, like the original.

I diffed them with ExamDiff and they matched so I open them in Notepad and they are different. Looks like white space has been removed as I originally suspected. Could also be an encoding mismatch but not sure how to check that. Here is what I see in Notepad
OK I can not post it as this editor is encoding it different then what I see. I will attach a image of what the 503 byte file looks like in Notepad

So it still looks like their FTP server is modifying the file.

I posted to FileZilla's forum describing the problem. Their answer is that files uploaded in ASCII mode are going to be changed as the line ends are changed to match the OS being used. I am uploading from a Windows computer and the Host site is on a Linux Apache server. I have always uploaded in Auto mode so that binaries upload as binary and ASCII files upload in ASCII mode. They said to try uploading in Binary mode only and my Host made the same suggestion. I did that and the site seems to work OK so far. I ran the Verification Tool after the upload and it found no modified files.

If you never ran into this issue I can only guess that you always upload in Binary mode or you are uploading from a Linux computer to a Linux Host or Windows to Windows. I have suggested your tool to several people in the Joomla Forum and have had no one come back with this problem so far. Did everyone start uploading in Binary mode only and not tell me?

Link to the FileZilla post
forum.filezilla-project.org/viewtopic.php?f=2&t=16108&start=0