also there are 2 different types of RCA's so if you are using the wrong one that could cause noise. figuring that out is hella impossible though so. other things i would try are
1 pico fuse mod if the HU is a pioneer
2 Amp ground. check connection's are tight and no fraying or touching wires anywhere. Ensure the paint is removed from the car ground location and if all that does nothing try a new location for the ground. With the battery in the trunk a direct wire to the battery is never a bad idea. make sure the wiring itself is good.
3 HU ground. try making your own HU ground instead of relying on the harness ground. If you are ballsy and have time run a 18g or larger ground to the amp for the HU.
4 RCA's make sure they are running on the passenger side. any power ground remote ect should be on the drivers side.
5 Amp theres a possibility you got a busted amp try it in a different vehicle or mess with it to see if the amp itself could be the cause
1 Sony head unit, no pico
2 amp grounds are good, tried diferent locations with no change, paint is all gone and grounds are on bare steel under a large bolt I also have a run of 1/0ga from my ground to the battery (-)
3 run of 12ga run directly to same grounds as amps.
4 RCA's are Soundrive HF, a coxaial cable made from 4 conductor Canre microfone cables, they really dont get mych better than thin for under $150, also emailed the amp manufacturer to verify the amp has single ended inputs (it does) as the single ended inputs require coaxial and differential inputs require twisted pair, rca cables are away from all other electrical (especially when I pulled the head unit and set it on the shifter, routed the rca 's out the front of the door, over the roof and in the back of the door, looped over rear headrest and straight down to my amp)
5 pulled the amp and put in a different one (with single ended inputs as well) and I get the same noise.