We haven't heard of this issue more. Can you explain a little more about what you're seeing? Specifically:
1) You can see the users in the "User Map" area of JFBConnect, but you can't see them in the Joomla User Manager?
2) In the User Map area, you can click on the Joomla user name and it should bring you to the User Manager with their profile open. Does that work?
3) Is the user actually logged into the site? If so, there must be a Joomla user created, but if it's not showing up in the User Manager, obviously something's missing.
4) Are you using any 3rd party profile systems (JomSocial, Community Builder) or any other extensions that are meant to modify the user's profile?
Answers to the above will really help us narrow things down!
Thanks,
Alex