I was given an AVI video that, although QuickTime Player could play it, ffmpegX could not convert it to H264 for iPod without messing up the A/V sync. The issue was the AC3 audio that QT said was using an "unidentified" AC3 codec. (But it did play in QT!)

I searched for some way to extract the audio and convert it. Audacity choked. DivX Doctor choked. Then I remembered another method I had used in the past.

I did an intermediate conversion using the DivX preset which has an audio preset of mp3. I set the pixel size and bitrate to match the source file. While the conversion "info" reported some skipped and duplicate frames, the result had good A/V sync.

I then used the H264 for iPod setting with my usual tweaks to maximize quality. Final result is in sync.

Thought this might help someone.