The thing is QT player is just playing back, Motion is doing a huge amount of heavy lifting, processing and compositing and it depends on your graphics card, processor and ram far more than the QT player. In Motion audio sync is given a very low priority because it is a compositor not an NLE. So you may be better served by adjusting your workflow to not need audio sync while in Motion or use another codec that is less processor intensive for working- such as the Animation or DV codecs and then render out to HDV when the project is complete.
Noah