Most of my TiVo programs have an AC-3 audio track but end up with an AAC (stereo) audio track after I transcode them to H.264 using a modified version of the iPhone profile. That's good for my iPhone/iPad (because they only grok stereo) but bad for my Apple TV 2 (which groks both stereo and AC-3). Apple handles the issue by including both audio tracks in the file but VRD doesn't have the capability to create two audio tracks out of one.
Handbrake can do it and, since my VAP workflow uses Handbrake for 720p files, my 720p files are getting two tracks and play AC-3 on the ATV 2 and stereo on my iPhone/iPad. My 1080i files are done in VRD so they end up with the lowest common denominator (stereo).
The issue is discussed here:
One approach suggested by hicmc is to use VRD to extract the original AC-3 audio and mix and group it back at the end using a 3rd party muxer (mp4box). Could it be done under the control of VAP?
It would help if VAP could at least extract the AC-3 audio track so I could remux it in post processing.