Are you using the built-in Joomla captcha?
I'm not sure why you're having that issue, but I'd honestly recommend disabling it from running on other forms than the standard Registration form from Joomla. By the time the user gets to the JFBConnect registration form, they've already authenticated through Facebook, so you should have high confidence that they aren't a bot. It's also one less hurdle for the Facebook people to have to deal with (another advantage of JFBConnect).
Hope that helps,
Alex