I have repaired permissions and run disk repair on the internal drive as well. Yes, I've played the clips in their entirety, but I'm going to do it again and look for any hiccups. That's an interesting theory and I want to check it out.
It has occurred to me that a workaround, although it by no means addresses the underlying problem, is to use QuickTime Pro to chop the clips up into several smaller files, copy them to the external drive, and then reassemble them via QuickTime Pro on the external drive.
FWIW, I neglected to mention (although I don't know if it's pertinent or not) that immediately after installing the external drive ten weeks ago I used SuperDuper to clone my entire internal drive onto the external firewire drive. I then erased the movies from the internal drive, which was bumping up against maximum capacity. I am able to boot from the external drive, and I want to retain this capacity should the internal drive (which is, after all, six and a half years old) fail.