My new iPod Movie 30GB copies video files randomly

I have a bunch of videos I encoded using ffmpegx 0.0.9 that are well within iPod specifications. I bring these videos into iTunes 7 and tell my iPod to sync my videos playlist. So here's what happens.
Either the iPod updates with all the videos, no errors.
Or, the iPod updates with only a couple videos, giving an error that the video is not supported by iPod.
WHY DOES THIS HAPPEN? It's so random and it makes no sense. Video.m4v will be fine one minute, update the iPod again, and iPod no longer likes it. Update again later, and it's back again.

Yes, it is normal for the iPod toi get quite warm with heavy use like gaming and videos.

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