After reading that -not- checking the Decode with QuickTime checkbox when encoding to H264 for iPod would result in a brighter (less dark) video, I've tried it with two AVI source movies. In both cases, I see a error id'd as "nonmono timestamp" (or something like that) in the info box of the ffmpegX Progess for that video; the resulting video is accelerated (no specific amount - varies with the vid) when compared to the audio. You end up with a video that slowly goes out of sync with the audio and presents a "white screen" for the last "X" number of minutes.

Checking the Decode with QT checkbox resolves the issue. I can't claim that this will always happen (and I think I remember it not happening with some other vids in the past) but there's something not quite kosher happening.

It would be helpful to know when I should expect this problem. I've attached the "info" for one of the source vids.