I am trying to convert my DVD to iPod.  I use "Magic DVD Ripper" to
get the file from my DVD to my PC.  Then I use either Jodix Free iPod
Video Converter or the "Convert to iPod" within iTunes itself.  This
works about half the time but the other half the iPod will have video
but NO sound.  I've determined that this is because the DVD has
"Muxed" audio.  But I have not been able to determine HOW to fix this.
 Is there a program that can convert a DVD file to iPod even with
muxed audio?

Hi, thanks for the question.

I think this should work well for you:

1- Copy your DVD to hdd;
2- Download DGIndex (http://neuron2.net/dgmpgdec/dgmpgdec.html)
3- Start DGIndex and open all the vobs which content you want through
the File - Open Dialog (after the first windows there's come a second
with add/del buttons);
4- Audio -> Decode ac3 to wav;
5- File -> Save Project and Demux Video (this should give you a wav
file with the audio in it and a .m2v video file);
6- Convert the audio using BeLight (http://corecodec.org/projects/belight/)
7- Mux audio and video.
8- Use iTunes to convert the video to fit iPod.