To truely see if thats the case...hook the system upto another headunit and see...if its still doing it I would think of possibly running the ground for your amp all the way back to the negative of the battery with 0-gauge if possible..
first, i would ground the head unit myself, and not use the factory harness for ground. i would also make sure my ground on the amp is sufficiently touching a good bare metal surface and bolted down tight.
ok i did check the ground and it bolt down and bare metal i wire brush on a drill and went to town on it. where would be a good place to ground the head unit off at without picking up road noise
Connect an Ipod or a portable cd player to the amp if you still get noise then it's on the amp side, ground, connectors, etc. If you don't then it's the HU