What would cause your alternator to reverse polarity?

This has recently happened to my 1996 Camaro after sitting idle for several years with a brand new battery (installed it to move the car to my new house). Knowing the battery would be dead, I took it in to be charged and the parts store accused me of trying to jump with the wires crossed. My other cars are a Prius and a Volvo. Anyone who knows those cars knows why I would not have attempted to jump a Camaro. Nevermind that the car was/is parked head-in inside my shop.

Anyway, I bought a new battery, hooked it up, turned the key on and the gauges pegged then, when I tried to start it, the battery posts began to smoke. Battery people have said it is possible to take a new battery and drain it to the end of its "useful" life (not a pun, as in the batter is no longer useful) which can reverse the polarity. Of course, a 1996 doesn't have a generator so it doesn't need arching but, clearly something is amiss!

I'll try and repost once I hear back from the mechanic.