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Well I had also a lot of problems to convert .mov files in aximcompatible .avi-files.
I use Quicktime Pro too, so I export the files to avi, with the highest possible settings. Then I convert them with VirtuaDub, use the sticky thread for a really good tutorial.
I'm using almost the same settings, expect i'm using divx 5.05 an sligthly higher bitrates, around 200-250 for movie trailers, they arn't to big anyway.
Hope I've helped you a bit.
btw. excuse my english, cause I'm from germany :).
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