I have had the same problem for years working out of FCP 6.0.x, on several different computers, with OS 10.4, 10.5, and 10.6, played on QT 7 and 10.
I still don’t know or understand why, but changing the sequence profile from “Apple ProRes 422” to “Apple ProRes 422 (HQ)” (then, of course, deleting all render files, re-rendering, and re-exporting) cleared the problem completely.
Thanks!