I'm inclined to think that there's a bad diode in the alternator. The diodes are what converts the A/C current to D/C current, what you are seeing is the wave pattern going from positive to negative. This needs to be addressed before running the engine again, as it can damage electronic parts and will kill your battery. I'd suggest changing the alternator, if it was a new/re-man part, look into warranteeing it out, as it is defective.
