I'd recommend double-checking your Facebook App ID and Secret key in JFBConnect to ensure it's the same as in the Facebook developer area. If so, there's also a setting in the Developer area in the Settings -> Advanced area for "Allow API Access to App Settings" that you should enable to allow JFBConnect to update your settings in Autotune.
With that said though, Autotune shouldn't affect your ability to share content. If you're having issues sharing, please let us know what those issues are.. are you getting an error or other message, do the posts just not show, etc?
Thanks,
Alex