Well they do take a fair bit of current to turn, so I'd expect a spark caused by large inrush current. How big is the power supply? It might not have shorted, just overloaded. The case is negative, that lug is positive. Make sure you're clamping only to the outer part of the lug and its not touching the casing.
2005 Yamaha Zuma YW50, 2009 Kawasaki Super Sherpa KL250