Start with the grounds
after that move to the equipment, disconnect stuff until it goes away, then reconnect stuff and narrow it down. I have seen this be bad grounds, bad amps, and even bad speakers or wiring. Just a bunch of trial and error. BTW: You did hook your 6v batteries up to produce 12v right? Stupid question, but something that may be overlooked. If you have it hooked up as a 6v ground system and the rest is setup as a 12v ground system, I could see that giving you some issues. Break out the multimeter and double check.