one thing that may be relevant though. did you encode the mpeg files to huffyuv using virtualdub? i just tried some footage that i had problems with in after effects but this time using DVD2AVI and the problem has disappeared, so i'm now wondering if its a bug with virtualdub.
Also i noticed something in the clip. the first lightsaber shot. Did you use my clip for that shot and overlayed your saber over the top of it?