Don't know how to fix it...but I quit trying to use Premiere to export quicktime files. I export an uncompressed quicktime and encode using Quicktime Pro. Huge difference in quality. I've tried a lot of different settings but I've never been able to get satisfactory results with Premiere.
As an alternate solution, you can use StaxRip , a totally freeware program for encoding Mpeg 4 solutions, including Quicktime 7 Mpeg-4 solutions (Xvid in an MP4 container with AAC audio)
Be warned, you better know the technical terminology for Mpeg 4 stuff and file formats.
Also if you encode as an mp4 format, anybody with quicktime can play it, and anybody with an mpeg-4 decoder in their media player can play it (*cough* linux people*cough*)
And by the way if you are using quicktime, I wouldn't even call it h.264, because when you encode a real h.264 file with any other h.264 encoder, quicktime chokes and doesn't read it. Quicktime is only capeable of reading the baseline profile, with limited settings.