I noticed this too. I have a number of quicktime movies that are 320x240 @30 fps. When I play them at full screen, they're unacceptably choppy (the sound is fine). When I convert them to MPEG1, the problem is gone.
<uninformed guess>
my understanding is that MPEG data is easier to scale, and to draw in general, than uncompressed (relatively) .mov files. It has to draw every pixel in the qt movie independently, but the MPEG gives it queues related to vectors and such
</uninformed guess>
Either way, I suggest you try MPEG. (I have used Media Cleaner Pro and the VCD codec that came with Toast Deluxe 5. With the (poor) source video I have, the quality of encoding is inconsequential)
-LL
Pismo 400 MHz G3
576 MB RAM