Some Movie Chapters Audio Not Sync'd with Video

i have discovered that a few of my movies (transcoded via handbrake) have chapters where the audio and video are out of sync.
i've restarted appleTV and computer.. no dice.
i restored appleTV to 1.0 and the offending movie chapters played fine.
after re-upgrading appleTV to 2.2 the out of sync audio-video returned in the same chapters as before.
i'm on version iTunes 8.0.1
anyone else found this and anyone fixed the problem?

I am having the same issue but with one wrinkle. I have two apple tv's and the audio syncs fine on one but not on the other. They are both running the same version. I stream all of my movies and I use handbrake also. It happens across different versions of handbrake. One thing i notice is that on every one that is a problem the movie plays for a very short time then the movie restarts. The audio seems to be off by about the time of the restart.

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