The only thing I can think of is to not use QuickTime for anything, not for exports, not for playback. (That would also mean not using ProRes.)
Apple iTunes store e.g. requires Apple ProRes for using videoclips in their shop. There is no way around this. Well, ok, that's Apple's policy, but most of the professional film studios use ProRes encoded Quicktime files both for delivering and for delivered material.
This is exactly what we do. We deliver movies for iTunes Store, so we have to go with ProRes and Quicktime professional for entering the metadata. Unfortunately, there is no other way around that if you work for them.
After doing more testing today, it looks that it is more a mac problem rather than a premiere problem... Keep you posted.
Well, it's true a lot of post places are using pro res for final ( not going to cine like at socal delux type place )
So, that said, this stuff like premiere pro and fcp, avid, etc is a bit on the low end in comparison...but everyone trying hard to do what they can in the market they have.
I think its worth noting that some post places I know that use FCP export mov with animation codec, from pro res....so maybe try this scenario from premiere pro ( extra steps and time but might work okay for you with sync etc )..
export as avi ( lossless )
then open in quicktime pro
export from QT with animation.
If the post place won't take THAT from you then at least you might be ' in the neighborhood' re: sync and so on...and they can either convert to pro res again or whatever... know what I mean ?