Peter,
I realize that you already have the MPG video, that is why I suggested "no compression" on the video format option. Also, MPG4 video is great-especially if there is a lot of motion or dissolves in the movie, but I have found as good and often better results with Sorenson Video 3. MPG4 audio is awesome, but if you are shooting for web viewing, for some reason a few Windows users will still have problems with it.
I am not sure if I am completely understanding your challenge...But, it sounds like the problem is that when you go to export the "movie to a quicktime movie," (not "movie to mpeg4") your option for the audio settings is not active? Can you look at the movie info in the quicktime app (window > show movie info) and see what the original audio codec is?
If the movies were originally compressed in a windows setting, could it be using codecs that may require access to a cross platform app like Adobe Premiere, AfterEffects, or even Media Cleaner to have the available resources to properly read your audio and convert it?
This sounds like a challenge that may need a phone call. It seems the writing on the discussion board is not accurately conveying all the issues you are up against. Sorry I wasn't better help. It originally seemed like a cinch.