I can only think of 2 real possibilities...
1) On the settings for both ATVs, under audio/video, do you have all settings the same? Also, do you have multiple audio tracks on said video or is it just the one?
I believe that the videos were avi's (old TV shows) so I believe only 1 audiotrack. They play just fine on my ATV2 (hooked directly to my plasma via HDMI) but not on my ATV3 (going through my receiver). Plenty of other movie rips play fine through the receiver, it's just these tv shows...I didn't change the settings when I used handbrake on them.
I just checked on my ATV3 (where the problem is) and under audio in settings, it says "auto"...the only other option is 16 bit. Dolby Digital can be either auto, on, or off.
I had this problem earlier with 2 different ATV 2s and the issue ended up being that I had Dolby Digital set to 'Auto' on one and 'On' on the other. My theater setup played the AC3 track while my bedroom one played the AAC track. I then found out I had screwed up the audio settings on that one specific file (every other one worked fine) and the AAC track was out of sync.
2) Is one going through a receiver/home theater in a box and the other going straight to TV? If so, which one is out of sync?
If you do have a receiver and that one is out of sync it could be a delay problem with the receiver itself. This can be corrected through the receiver normally by checking for a delay function and having the video be delayed by however much is required to look normal.
On the ATV3 hooked via my received, the auto also sounds "rushed" for lack of a better term - likes it's playing slightly too fast (voice pitches too high), but again, this doesn't happen with other movies that I've used handbrake for with the same settings...
