Allow files with 5.1 surround sound to be converted correctly (i.e. AC3 passthrough). From the original source code handover notes:
For QuickTime files, the Apple TV recognizes AC3 data with an "ac-3" audio atom. For MP4 files, check the work the HandBrake team has put into AC3-in-MP4.
One of the last releases of VisualHub introduced dual-audio files. Meaning, one video track, and two audio tracks - one stereo AAC, one surround AC3. I accomplished this by modifying Johan's movmux tool (disabler) to properly construct a .mov file to the Apple TV's liking from a h264/ac3 .mov file and a stereo AAC .m4a file.
Because of channel-order problems with ffmpeg at the time, re-encoding AC3 wasn't a viable option, so only proper AC3 audio tracks could be used and passed through.
It doesn't seem like the VisualHub method is terribly efficient. For one, most tagging programs (parsley included) have problems with the MooV container. Subler is pretty effective remuxing multiple audio tracks into a single m4v file (which is also the way apple does it).
I'll play with some ffmpeg options and report.