It may be an MP4tools issue. The just uploaded version 3.2.2 fixes a bug that sometimes caused freezes on the ATV, usually files with AC3 audio and and added AAC track. I'm not sure of the cause, but the new version fixed the bug that I could duplicate. Give it a try before you waste too much time fiddling with your receiver

. BTW, I've got a Yamaha receiver and have no issues with AC3 audio, though there could be something up with your settings on connections. For the ATV, I've had the best luck setting Dolby Digital to ON not Auto.
I hope this helps. Cheers.