Sounds like you have a ground loop.
Do you have an amp powering you mids or only an amp for your subs ?
Either way I would try eliminating the ground at the HU.
Make your own ground so that you are not using the ground in the factory harness.
See if that fixes your problem if not, then try relocating the amplifer ground.
I've heard of this before but never witnessed it first hand. I've heard this is caused by the manufactuer using a common ground point for the brake and the HU. The HU picks up the noise and passes it on.
92 Bonneville SSEi - Stock - Remaining repairs needed due to neglect by previous owner - ABS/Trac, AC.
Mods so far: Maganflow High flow Cat, Rebuilt */C
Future Mods: Interior swap for Leath, High Output Altenator, Crazy system, Climate Control swap & Custom Exhaust/Intake.
98 Dodge Stratus - Wifes Daily Driver
92 Dodge Shadow - My Winter Beater