Best answer (Chosen by asker)
This is caused by 2 different things! 1. A damaged Video Stream and 2. The audio source was loaded from a seperate file.
The first thing to remember is NEVER extract a wav with VirtualDUB from an AVI and use it as your audio source, most of the time the audio goes out of sync, instead decompress the audio. Do the following with VirtualDUB...
1. Click Video - Direct Stream Copy.
2. Click Audio - Full Processing Mode.
3. Click Audio - Compression. Select <No compression (PCM)> and click ok!
4. Click File - Save AVI and try it with TMPGEnc.
And as I said earlier, it could be a damaged video stream, in which case you might want to try AviFixed or DivFix to see if they can come up with anything.
NOTE: Always make a backup of an AVI file before running it through AviFixed or DivFix!

