only thing I can think of is to hook an ammeter up to teh alt and measure the current it produces. does it do this even with the lights off? maybe the problem isnt showing at idle in the shop cause there is hardly a load on the alternator. maybe take it back to the place and turn your lights and stuff on so it starts doing it, then have them test it?
either way it sounds like the alternator is producing enough juice to run everything, but it is spiking and acting odd. i still suggest swapping a new one in, keep the receipt of course

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