I have a similar problem with my car (stock Mach460 + CD changer + 2 10" subs run off of speaker level inputs)
My problem only happens maybe 40% of the time. It sounds like a humming noise that comes thru the speakers, and the humming is independant of radio volume. I can turn the radio volume to zero, and the buzzing sounds the same as it does if the volume is really loud. The only way the buzzing stops is if the radio is tuned off. Also, the buzzing's frequency is directly proportional to engine RPM. So I'm guessing it has something to do with a bad ground, and the altternator maybe. ???