hi Will,
I do doubt that this is indeed relevant to your probs, but the symptoms
are very much like something that bites me occasionally (and it always
freaks me out until I remember). Do you have 'CPU Frequency scaling'
enabled in your kernel(s)? I do, but I have scripts etc that are supposed
to semi-automatically switch to the 'performance' governor whenever I'm
doing audio related stuff. Occasionally, when things are getting
experimental, I can finish up running jack etc with the 'ondemand' governor
still active, which inevitably results in the sort of performance you're
describing. Just a thought.
cheers, Cal