Use Gspot video utility to determine what type of audio is in the new avi's. Might compare it to what is in the old ones too.

A lot of newer avi files seem to use vbr mp3 for audio, and it can cause problems. Been a while since I've used TMPGenc Plus, so I don't remember if it is a problem for this program in general.

You could save the audio as wav files using VirtualDub, process the avi to mpeg in TMPGenc using the ES Video only setting, then remux using the mpeg tools in TMPGenc.