Most of the videos I'm having issues with were encoded by someone else so finding who did 'em is going to be tricky.
What's most frustrating is that it all used to work so well!
I can (don't know that it will help) send along analysis of the "good" vs. "bad" files as seen by a utility I have called "VideoSpec".
I sure can't find any rhyme or reason regarding encoding vs. bitrate vs. image size vs. interlacing which seems to line up at all with the things that don't play well. That's what is so maddening.
Example: This plays well:
*** General Parameters ***
- Name: 04.Race.MotoGP.720p.mp4
- Container: MP4 - QuickTime
- Size: 1.922 GB
- Duration: 1h 5mn
- Bitrate: 3 907 Kbps
*** Video Track Parameters ***
- Format: H.264/MPEG-4 AVC
- Bitrate: Max.: Undefined / Average: 3 743 Kbps / Min.: Undefined
- Frame rate (fps): Max.: --- / Average: 25.000 / Min.: ---
- Encoding profile: High@L3.1
- Image size: 1280*720
- Pixel Aspect Ratio: Undefined
- Display Aspect Ratio: 16:9
- Interlacing: Progressive
BUT this does not:
*** General Parameters ***
- Name: Comedians in Cars Getting Coffee, Louis C.K..m4v
- Container: M4V - QuickTime
- Size: 321.91 MB
- Duration: 22mn 39s
- Bitrate: 1 894 Kbps
*** Video Track Parameters ***
- Format: H.264/MPEG-4 AVC
- Bitrate: Max.: --- / Average: 1 600 Kbps / Min.: ---
- Frame rate (fps): Max.: 30.303 / Average: 29.970 / Min.: 29.412
- Encoding profile: Main@L3.2
- Image size: 852*480
- Pixel Aspect Ratio: Undefined
- Display Aspect Ratio: 16:9
- Interlacing: Progressive
The smaller, simpler 2nd file causes the ATV to skip frames, eventually no sound and then the video drops out entirely. The larger, more-complex first file plays just spiffy from start to finish.
That's the best I can do for file information. I'm happy to run these and others through whatever tool would give you the best information to look at (and to email if you prefer getting it that way).