Can you check a few things and let me know the answers?
1) What is your setting for "User Creation"? Full Joomla Users or Facebook Only?
2) What is your setting for "Automatically Link Facebook Users by Email"?
3) Can you check the User Map tab in JFBConnect to try and determine if the user's Joomla account that has the same email address is listed there? This will help us determine where in the process something broke down.
4) Can you you let us know what User plugins you have enabled on your site?
5) Are you using any SEF URLs on your site, and if so, what are you using to generate them (Joomla core SEF, sh404SEF, Artio, etc)
Sorry for the spew of questions, but that's not an issue we've heard of. Obviously, that's a bad thing to happen though, so hopefully, with the info above we can figure out what may be wrong quickly.
Thanks!