Hasan,
There's a few reasons that the comments wouldn't transfer. Mainly, while each page's URL may be the same, the Like button that's generated by JFBConnect or by SP Comments may not always be the same as what you see in the URL bar. I don't know how SP Comments generates the URL for Like & Comments, but JFBConnect does a lot of work to try to make sure the best URL is always generated in a lot of environments.
For example, many pages in Joomla can be reached through multiple different URLs: SEF, non-SEF, blog view, extra query string parameters like page numbers, etc. JFBConnect will eliminate a lot of those variances so that the same comment box will properly appear on multiple different URLs for the same content. That also means that the current URL may not be the one that JFBConnect is generating.
That information, combined with what SP Comments may have been doing, simply means that the comment box JFBConnect is generating may be referencing a different end-URL than SP Comments was.
To fix, you may need to turn on SP Comments again, determine what URL they are using creating and then explicitly use our {JFBCComments href=http://site.com/...} tag to place the right comment box on pages where comments were lost. For new comments, just rely on the JFBCContent plugin or tags to use our URL-structure.
Hope that makes sense, but if you still need help, just let us know,
Alex