Some .mp4 files in my iTunes Library won't play on latest AppleTV, but will on my 3rd Gen AppleTV

Some .mp4 files in my iTunes Library won't play on latest AppleTV, but will on my 3rd Gen AppleTV. Furthermore, the files that won't play WILL play on the latest AppleTV IF I play them through the PLEX app. Go figure. Obviously Apple has left something out of the latest AppleTV that was included in the 1st, 2nd, and 3rd generation AppleTV. The Apple development crew should be ashamed of this. Having to use a 3rd party app to play videos you should be able to play with Apple's own app, but won't! Shame! If Steve Jobs were still around this would have never happened!

If I run the .mp4 file through Handbrake it will play with no problems. BUT, this solution would require me to re-encde more than half of my entire iTunes Library! Not acceptable! So I have two choices. 1. Only use PLEX to play my video files stored in iTunes. 2. Take the new AppleTV back to the store, get a refund, and go back to using my 3rd generation AppleTV. I'm leaning towards the later choice.

Does anyone out there have a better solution to this problem? If so, please share!

Thanks!!!