JFBConnect doesn't alter the normal registration process through Joomla in any way. If your users are registering through Joomla/Virtuemart directly and not through JFBConnect at all, then if the password is missing, I don't think that would be caused by JFBConnect.
To test, can you try disabling the JFBCSystem, JFBCUser, and JFBCAuthentication plugins. That will completely disable JFBConnect. Then, try registering again. If the password isn't shown, then that means something else is preventing it from showing.
If it works then, let us know. Again though, there's no reason that JFBConnect should be altering 'normal' Joomla users. Our extension simply wasn't designed that way.
Thanks,
Alex