What settings are you talking about? Do you mean in the FB App area of Autotune? Those are all based off your current URL. If you changed the URL since when you originally ran Autotune, then the URLs will be out of date. You'd need to use the Refresh button to re-run autotune. However, that requires an active subscription to fetch all the latest settings.
The alternative is to manually edit your application in the
developers.facebook.com/apps area. You'll need to update the domain and site information there.
Most importantly though, if the login functionality works on the front-end, you should be ok. Autotune just checks and helps to configure things, but it's not required to be used. You do not need an active subscription for JFBConnect to function.
Hope that helps explain,
Alex