Have you tried to re create it. In this case weather it is HD or SD is not the issue, it is not a bitrate issue. Again, the issue is what looks like a hold frame. When framing forward and watching your burn in counter, I can see the frame counter is moving but the quick time has a bunch of hold frames which give it that strobe feel. I think it is a bug in CS3. Again, just try to set this up SD or HD in AE8:
Comp is 23.98.
Image seq is imported at 23.98
23.98 Frame counter to help verify the frames.
Start image seq at frame 2 of comp.
Render QT photo jpeg.
Again, this same set up works perfect when the image seq starts at one, it only strobes when images seq starts at frame 2 of comp.
I have tested this on three diff systems, and one being a mac.
AE7 is the only one that will render out a 23.98 QT the way I have it set up.
I just want to verify that other people are getting this hic up.