Have you set the speaker configuration first before setting the auto cal running. Still it sounds strange the amp tunes off. undo and redo the wireing connections too. Maybe check the ohms of your surrounds. It might be a safty thing tuning off or I might be talking rubbish *biggrin*
I'm pretty sure I once got this and I found a stray wire which casued a short. Likewise it only occured when trying to calibrate the speakers. Unplugging everything and adding cables back in gradually is a good way of finding the source.