Could you show us at least a small part of your clip?
It is not easy for us to determine the cause of your problem without seeing your clip.
Try this for now:
Open your movie in QT then go to Window>Show Movie Properties
Highlight the video track, click on the Visual Settings tab.
In the Transparency menu select "Straight Alpha".
Play your movie now and let us know if things got better or not.
What is your frame rate?
Salut,
Serge
Invigorator/Proanimator Training:
http://library.creativecow.net/articles/hamad_serge/invig_training.php