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I've been having the exact same issue and have spent months trying to fix it, trying out every possible codec and settings combination that Flash has.

The quickest "solution" is to make the flash...

in the quicktime export dialog, there are several different places where you can set the movie dimensions. If you go to the "quicktime settings" area, you might have different movie dimensions there,...

Try changing the codec. I found that using the H.264 codec you can get a .mov that is identical in quality to the .swf, with a relatively low filesize. (a few dozen mb compared to a few hundred mb...

I have a different problem with exporting, but in searching for answers I've stumbled upon several people with the same problem (and also fix!) that you have.

Try these two links out:
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