Ahh. Yes. If you're using a different logout button than ours, it won't log the user out of Facebook, even if you tell JFBConnect to do so. In that case, you can't enable Automatic Logging in, or else the user will never be able to log out of your site.
If you can modify that module you're using, and update the button, you can simply add
onclick="javascript:jfbc.login.logout_button_click()"
That will make things work just like our JFBCLogin's logout button will work. Hope that helps, but if you have questions, just let us know.
Thanks for the kudos on 3.2. It took a lot of work (and testing), so we're glad to finally have it out the door!