Take the amp out and make some test cables for it so that you can set it on a fender or something convenient near the battery to test it. I went through some weirdness like this a few months ago and it turned out that the spot I chose for grounding was no good. I had alternator whine, amps would cut in & out while driving sometimes, sometimes the amps wouldn't power up, eben started smoking one of the amps. Changed my grounding location and everything cleared up. When you're troubleshooting, you want to deal with one component at a time and verify that it functions...sometimes it's best to remove it from the environment that it's in so that you can eliminate installation errors/glitches.