In answer to the question of does it happen with the quick shift fitted, it does! Happened to me a few times. It seems to happen if you don't make a totally positive gear change. I think the system works by comparing road speed to engine revs and works out the gear form there so if you fluff the shift a bit it loses its reference and takes a while to sort itself out.
As others have said it normally takes a few seconds to settle but sometimes you have to switch off and back on again.