I've encountered audio-encoding problems myself, especially with VBR MP3 audio (from AVI sources).
If everything else fails, just extract the audio stream (e.g. with VirtualDub), convert it to MP2 and multiplex it with the video stream using TMPGenc tool.
I found that I could convert most sound formats to MP2 using BeSweet (whew. lotsa setting there...).
MVP works fine up to 192kb MP2 and is as simple as it gets. (latest and last version is 1.2 I believe)
As for gradual synch problems I've not yet found a way around using an audio editor and streching/pitching the whole audio stream (CoolEdit or Sonic Sound Forge for example).
There's a guide for doing this on
www.vcdhelp.com under the topic "Edit".