Some Audio Not In Sync When  Movie converted from .avi to .m4v

I've downloaded videos in avi format and then converted them to m4v by using Export in QT Pro and selecting AppleTV with default settings.
The avi version plays ok right to the end but the m4v loses audio sync by about 1-2 seconds but only in the last 5 (approx) minutes of a 40 minute video.
Any way round this or should I look to convert with a different application?
Joe

The issue seems to be related to sample rate. Because there's no 'options' screen for the Apple TV quicktime preset, there is no way to correct it on the front end that I can see yet, but in the cases I have had I was able to correct it this way:
open the out-of-sync mp4 in Quicktime. Select 'show movie properties' from the window menu. Select the audio track and hit extract. Select Export: Audio as AIFF when the new untitled audio clip opens. Click 'Options' and change the sample rate to 32khz. after the audio clip exports, open the new exported audio clip in the quicktime player. Select all, copy, then back in your movie, select the whole movie, then pick 'Add to Selection and Scale'. You can then save the movie as .mov. I haven't tried exporting to Apple TV again, since this would typically take several hours, even though the video format should be unchanged.
I tried to simply change the audio sample rate and save in Mpeg Streamclip, but the resulting file was invalid.

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