That's strange and not a problem we've heard of before. First, if you're using the JomSocial registration flow with JFBConnect, then the activation skipping will not work. Since they are going through the JomSocial registration, we can't override the activation that is performed at the end of that flow.
If you're using JFBConnect for registration or automatic registration, it should work though. If that's the case, please let us know any other user or authentication plugins you have enabled. It's possible one of them is interfering with our registration process and not allowing activation to happen properly.
Thanks