Very possible that it is a bad ground. Just to make sure, do you have a power/ground wire running along your RCA's? That'll cause an alternator whine.

 

RCA and power on on opposite sides of the car. Amp ground is a 3 foot length grounded to a large hole drilled in the floor board with a large bolt and Star washer on bare metal.

Headunit is grounded to Maestro RR and Maestro RR is grounded to the factory harness.

So it is possible grounding RCA shield to headunit case will solve issues other then blown Pico fuse? All I ever see is it is a solution for headunit issues.

 

Give the head unit a real ground and see if it helps.

 

This. Factory grounds are usually not very good, and even a small difference in ground potential between the amp and headunit will cause whine.

 

The pico fuse is blown inside the radio, the rca got shorted to ground or maybe you hot swap them.

 

I'm sure the headunits factory ground has recistance that is high compared to the amps excellent ground. So hu and amp have different ground potential. When you connect the rca shields to the hu the hu shares the amps ground through the rca shield and the ground potential gets (more) even and the noise is minimized.
I would expect any decent car audio shop to know this, it's basic electric knowledge.
But the shop probably would earn more selling you a new hu...