This may be not what you're looking for at all, but maybe try to render them as .tga sequences instead. Bring those into, say, After Effects and render a .mov from there. I prefer to render .tga sequences because they are pretty much lossless and it gives much more freedom/quality in the end. And I THINK it will also render faster, because compression takes time.
I've never rendered Quicktimes from Maya, so I can't tell you how to fix THAT, but this workaround should work.
http://www.fireinthesole.com/
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