I searched around and wasn't able to find anything that answered my question directly. I've got an AVI file (Xvid Video; MPEG-1 Layer 3 Audio), that will play audio no problem. However, once it's been run through TMPGenc (tried MP2 and PCM audio), the resulting audio file doesn't make sound. I tried decompressing the AVI first, then using TMPGenc, but to no avail. I also extraced the audio to WAV with VirtualDub, and then to MP2 using BeSweet. I figured I could load the M2V file and the new MP2 file into TMPGenc Author, and I'd be alright. However, it said the audio format wasn't supported. I didn't want to attach the WAV to the M2V due to size limits. Finally, I used Cucusoft first to make DVD compatible files, and the audio worked fine, but I wasn't happy w/ the video. Sorry for the long-winded post, but I'm lost. Oh, and I've gone through the codec tutorials on here, and I'm almost certain I don't have any conflicts.
If the audio in your avi has a sampling frequency of 48000hz it needs to be converted(unless you've done so already). Another thing you can do is take the movie with the bad video and de-multiplex the audio with TMPGEnc(File>MPEG Tools>De-multiplex). Then mux the good audio with the good video using "Siimple Multiplex"(again, using MPEG Tools).