Regarding interrupts, GIE isn't disabled when handling an interrupt, so interrupts can be interrupted. But if I do set GIE=0 then that causes enough disruption to the USB stack in terms of timing delays while waiting for the servicing that is chokes and disconnects. I'm not worried now as I have solved that sufficiently that it no longer disconnects and the result capture hasn't so far had overruns related to not being service quickly enough.