In the case that you're connecting a user, are you using the "Connect User" button in the JFBCLogin module, or some other method?
Do you have the "Automatically Link Facebook Users by Email:" enabled? This setting is used if someone isn't currently logged in through Joomla, but tries to connect through Facebook. If their email address is in the system (with a Joomla user), this setting will map them together. This setting is -not- required for the Login module's 'connect user' button to work.
This doesn't answer your question at all, but hopefully gives some insight into how things should work. If you're trying a method outside of the above, please try the above to see if it works as expected. Either way, we can try to get it working how you want, but it's good to get a baseline for what is or isn't working properly right now.
Thanks!