You'll need to edit the /components/com_jfbconnect/includes/jfbconnect.js file. Search for "self.location" and you'll find a line like below:
self.location=jfbc.base+'index.php?option=com_jfbconnect&task=loginFacebookUser.......
Update that self.location to top.location and that should work on the main window, not just the inner iframe.
Let me know how that goes, but if you need anything else, we'll be here.
Thanks,
Alex