Okay let me have a think about this, in the meantime could you let me know the following:
iMovie or FCP?
1080i 50 HDV?
Does it have the same stuttering or slo mo effect when you play it as a self contained movie in QTP?
What version of QT were you using?
When you scale up the picture (Full screen) does it get worse?
As I have edited a lot of HD footage in FCP and have only seen the effect on slow pans in 720p and complex images in 1080i 50.
As I said just curious?