1st off, its only occuring in the woofers, or does it occur in the comp amp as well?
if it happens to the comps and the woofers, you know its not the amp/amps...
sounds like ethier a grounding problem, or some transistors are bad...
willing to bet its a groudning problem... i wrote an artical on proper grounding techiniques and how to minimize the chances of induced noise VIA grounding...
without getting technical bad connections often get worse over time, and there is a point to where the resistance affects the output...when the current flow is great enough it finds the path of least resistance(bad connection= high resistance).. chances are its feeding back into the output (hence passing threw the woofers) swiching supply BACK threw the transformers to ethier the amps ground, or RCAs.. or vice verser .. easy way to tell if its the h/u, is unplug the ground wire(disconnect the rcas and REM from your amps before hand) and see if the deck still powers up threw the antenna(make sure the antenna is connected).. if the deck says on/or tries to its a bad ground via the h/u...
when i install a after market system i always reground/bypass factory wiring because its usually poor..
Im willing to bet you simply have a bad ground on your h/u though or may be a crossover(active stand alone units do this sometimes as well