For the manage_pages permission, there won't be a login popup like you may see normally. You'll be redirected into facebook.com and the popup will be in there. After accepting, you'll be brought back to your site.
Easy next step: Logout of Facebook.com and then re-authenticate on your site.
Harder next step:
* Go to the Facebook Explorer debug page:
developers.facebook.com/tools/explorer/
* Make sure you're logged in with the right Facebook user for Page/App
* In "Application" drop-down, select the app for your website
* Click the "Get Token" button and then "Get User Access Token" in the drop-down
* In the middle section, make sure the "Manage Pages" permission is checked.
* Hit "Get Access Token"
Then, logout on your site and re-authenticate again. At this point, you should absolutely have the manage_pages permission.. if it's still reporting it's missing though, let us know and we'll keep digging in.
Thanks,
Alex