It's not the QuickTime viewer, per se. It's the part of the QuickTime system that renders images for playback---which is used by the media player known as QuickTime Player, by Final Cut Pro 7, and even by our software for some (but not all) QuickTime/.mov formats.
This moving target of QuickTime's inconsistency with colors is one of the reasons that we gave up on trying to use the QuickTime infrastructure for decoding many kinds of .mov files; and we're gradually replacing our dependence on QuickTime with our own decoders.
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Todd Kopriva, Adobe Systems Incorporated
After Effects quality engineering
After Effects team blog
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