I have a fairly extensive library of transcoded video of mp4 (h.264/ac3), that I can fairly easily demux into separate streams and transcode the audio to AAC to get video that will sync with my iPod touch using iTunes. Most of these files are 720x480 DVD rips that have the SAR set to 40:33. The remuxed video display fine on the iTouch (using mp4box). Even if I decide to remux with softsubs. This is all done using the -ipod flag in mp4box.

Now, if I try to remux these video with two audio streams (AAC first and then AC3), then the SAR flag is ignored and a 3:2 aspect ratio based on square pixels is applied. This is again using mp4box but just adding a second audio stream to the mux command line. These will sync using iTunes, they just play back at the 3:2 aspect ratio.

Does anyone have any experience muxing .264 video streams with both AAC and AC3 audio in a mp4 container for playback on apple devices? I suppose I could always transcode the DVDs again to 720x400 to avoid needing a SAR setting, but I find that annoying since I have so many files that I would need to re-transcode. Plus I would rather avoid resizing if possible.