if QT is scaling your video at all for playback it will screw up graphics like that too. I know when I export something from FCP that is DV, if I watch it in QT it usually looks like crap but, if I export from QT as a .m4v or another format for web, it will look fine again. What is the final output for the video you are working on? You might try taking it to the next step and see how it looks there…