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Try Project Settings/Match Legacy AE QT Gamma Adj
You may wish to convert the file in QT Pro rather than in AE. These issues have been reported over and over, yet the exact cause of the problem never became clear. It seems to be an issue with some hardware- accelerated routines in QT's encoder in combination with certain setting (the problem does not occur everytime).
This is an Apple bug. H.264 rendered from both AE and QuickTime Pro on Windows both lack in contrast when viewed in QuickTime Player. Drag it into a web browser window and you will see that Apple's QuickTime plugin applies the correct gamma values.
- Jonas Hummelstrand
you can also try and disable directx acceleration in the quicktime player itself. this will only fix the problem locally though...