Sounds like the issue was with the amp.
Sorry damelon, but I'm posting part of what you put in your AVS thread just for some sort of update/closure here.
...has a fault in the amp which is causing the DSP to crap out somehow. Sub just randomly distorts and after swapping woofers between subs, testing cables, etc we have determined the problem resides in one of the amp back-planes. So off it goes to Axiom!
2-M60s, VP180, 8-M3s, SVS 20-39PCi, DIY Sub, 8-Shakers, JVC RS45, Anthem MRX-1120