I'm not exactly sure what you mean, actually. When the user's Joomla session expires, the user should definitely be logged out, regardless of whether they logged in with Joomla or with Facebook / JFBConnect.
As for clicking the Login With Facebook button, that will bypass the username/password popup if the user is already logged into Facebook. There's no way for us to log the user out of Facebook without them clicking the Logout button on your site (and you have the Logout of Joomla Only setting at 'no').
Hope that explains if I'm correct in what you were looking for, but if not, let us know! Other than that, very, very happy to hear JFBConnect is going smoothly for you. We work hard to have powerful features that are easy to use. We don't always hit that target, but are always looking to improve. Any feedback you may have is always welcome!
Thanks,
Alex