I am having exactly the same problem with AE 6.5 and FCP HD 4.5. My clips generated in AE and rendered as QT mov files look great in both of those applications. The edges get sawtoothed when I bring them into the timline in FCP HD. My QT renders out of FCP retain this jaggedness.
Have you figured out a solution for your clips yet?
I’ll keep you updated if I find anything out on my own.
Thanks
Michael