Something all of you may have missed, and an easier fix than any listed.
The exact same thing happened to me in my HT when I added seperate power amps to a receiver, what the problem was was having a dimmer swich on a lamp (or wall) in the same line. The amount of noise made by a dimmer switch is often not picked up by a receiver, but will be when seperated power amps (as in your sub) are connected. Power conditioners didn't clean it up either. Switching from a lamp with a dimmer to one without immediately stopped this problem completely!
If this is the problem, it's simple to fix-kill the dimmer switch, if not, you may need to advance to some of the other rec's above....