The voltage regulator in the alternator doesn't just regulate the voltage for the change in RPM's but it also regulates the voltage for the load on the alternator, more current draw will cause a drop in voltage so the regulator will adjust to try to keep the voltage constant. There's a chance the regulator is bad and over compensating for the load. If it just happened with this amp then there almost has to be something about it that is causing the problem, though it's hard to imagine what it would be. I'd try switching to a different amp if you can to see if it makes a difference, if it doesn't, have your alternator checked out.