I’m not experienced with QT animation. But checkout the field order of it. And make sure AE interpret it acordingly?
Whenever I have a problem like that I divide and concour.
Look at the QT is it good? If not then theres your problem.
If it is ok – then try and load the QT into a comp and render it out. What happens?
Is it good? If not, then you have a problem with the field order interpretation, or your render settings. Make sure the field order is kept cacordingly all the way through your workflow.
If its good, then precomp the comp with the QT and render it. Is it not good – then do the same thing you just did with some other media. Try and find out if the error is consistant or only in relation to that specefic QT animation.
If it’s the QT, the find on wich point it differs from you other media that worked and see if that would lead to a solution. And so on and so forth.
I think your problem is not After Effects or the QT, but the way you face your problem. Look at it in steps and you’ll solve it.