Make sure you are using a distribution profile for submitting apps to the App store and TestFlight. Before Apple bought TestFlight, they would only accpet apps signed with an Ad Hoc profile (which doesn't have the beta entitlement). Now that TestFlight is owned by Apple, developers build their app builds for app store submisssion using their Distribution provisioning profile, then after they submit their build they have the option of directing the submission to TestFlight or the App store.
This is a good hint, and I double checked and can confirm that I am actually using the proper distibution profile. It is the exact same profile that I have been using for my past 30 or so TestFlight builds. So I don't think that is the problem.
Also, I am pretty sure that the submission process (when you hit Upload to App Store in the Xcode Organizer) will tell you if you are not uploading with the proper profiles.