Sorry, I can't be of much help. The files that I download are always either AVI or MKV. However, if you get Visual Hub to get you the TV compatible video in MP4 (using the -an), then you may be able to convert the audio using besweet or something similar. Then afterwards remux using MP4Box or Quicktime Pro.
Thanks again. I'm trying a straight save as in Quicktime for the wmv. I'm not sure if that will do anything for me, but it's worth a shot.
As for the 5.1 mkv transaction-- I converted it to mp4, with audio passthrough, then I demuxed the audio out of the mkv with mkvextract, resulting in an mp4 and an aac file. So far, so good. However, using MP4Box yields an "Invalid IsoMedia" error when trying to reference the .mp4. Am I doing something incorrectly?