I had that problem with asf's but not avis try running it through virtual dub then putting it back in TMPGEnc. Or try downgrading to a lower version of TMPGEnc that might help.
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Win2K has a stupid preview option that lock the file.
Be sure you don't have the preview of that file in some explorer window.
(When I open mpg files in PowerDVD, if the preview is active, I have an "Unsupported resolution" error ^__^!!!)