JFBConnect is fully compatible with the the newest versions of the Facebook API. As a matter of fact, all apps that are created automatically are forced to use the latest version of the app and can't downgrade to older versions.
We usually set JFBConnect up to use the older version of the APIs as the older versions usually allow more access. That's going away slowly, but it doesn't hurt to set to the older version as it allows JFBConnect to access some of these 'older' features on apps that were created long ago, but as mentioned, we're still compatible with the latest releases of the API that Facebook may force your app to use anyways.
I hope that all makes sense to explain the background.. you can set the 'Upgrade All Calls' setting however you want and you likely won't see any difference in behavior.
Thanks,
Alex