Figured it out in the end - the internal virtual circuitry could not take the volume levels so were clipping. All I had to do was do a vol $1 message with a float down to 0.9 going into the jit.qt.movie . Then I just cranked the volume up on my sound interface to compensate and bingo! No problems!
I just went through fiddling with this, and it turns out using regular jit.movie for audio is pretty sketchy .
There is definitely some nasty internal clipping stuff going on if you leave jit.movie at default volume, and it does seem to be mostly bass that causes the problem. You can try and compensate by setting the volume lower (I found .7 was fairly safe) However, if you use jit.movie~ and build out an MSP output solution, it does completely solve/avoid the problem.
It would be nice if the default volume of jit.movie wasn't causing the problem, since there are times I'd like to play audio from a movie with as little processing/alteration of it as possible.