I know you said you checked the grounds, but you might want to double check it with this test.
RCA's provide a ground link between the deck and the amp. If there is any current running through that link then you get noise in the signal.
Here is a test you can try to check your grounds. Do this with the radio on and the whine present.
Get a 20ft small wire. Attach/clamp one end to your neg batt terminal. Attach the other end to the neg voltmeter lead. Set your meter on DC volts. With the red lead, check for any voltages at your amp ground points, you may also want to try your deck ground point.
You should see something very close to 0v. But if you see anything strange, even a couple of mV. That could mean a voltage potential exists. Sometimes an amp takes care of that potential by grounding through the rca's.
Did you ground the rca's at the deck? If the excess current is coming from the amps, then the signal is already damaged by the time the rca's ground out at the deck. You might even want to try grounding them in the back also.
Hope this helps.