I posted this as a reply to someone else in the ffmpegx forum but I think I should have made it it's own thread:

Does anyone know if there is a bitrate limit on AC3 audio and the Apple TV? I've got quite a few HD movies I used Visual Hub to create MOV files with AC3 audio. All but 3 of them work just fine. The 3 that don't work play the video flawlessly but the audio is gone or I get occasional hisses and pops. I've discovered that the 3 in question all have audio bitrates > 448 Kbps. Do you think it's a limitation of the Apple TV... or maybe my A/V receiver?

Are there tools on the Mac to mux/demux MOV files? I suppose I could try extracting the audio and encoding it at a lower bitrate.

Any suggestions are appreciated.

Edit: The movies play fine in iTunes/Quicktime on my Mac. It's only when played through the Apple TV that the audio is gone.