That's a
well-known issue with h.264 gamma shift in the Quicktime player. You've verified that the video is correct in AE and windows media player so the video is fine. If you have dual monitors, you can position the QT player so it's partially in both monitors and sometimes the gamma shift goes away. It's weird. Anyway, it's just a quicktime problem. You can check google for more info, there's plenty out there.