Well, the first thing you're doing wrong is using a 1280x768 raster size. Did you mean 1280x720? I wouldn't be surprised if oddball things happen when you try to do something non-standard.
The second thing you're doing wrong is using the "Quicktime Conversion" feature. What you should do is export a Quicktime movie ? not a reference movie ? of your timeline, then run that through Compressor to convert it to your delivery format. I can give you more specific advice on just how to accomplish that if you elaborate on what you're trying to do.
Whether either of those "wrong" things is behind your problem, I can't say, but I figured we'd start somewhere.