The main reasons that your site appears in the pop up is if you're Connect URL in Facebook is set to www and you're trying to access the non-www version. Not sure if you checked out the Common Support Questions, but try the 2nd point in there (which then refers you back to the forums here).
www.sourcecoast.com/extensions/jfbconnec...on-support-questions
Also, ensure that the JFBConnect User plugin is ordered AFTER the Joomla user plugin.
If none of those work, let us know and we'll come up with more solutions!