You have a ground loop. This creates a path for current to flow around your system (through the RCA lines). It then causes these lines to pick up interferance.
One is the dim dip relay buzz (day running lights). The other is the ignition system (pitch changes as you rev the engine) etc etc it will pick up it all.

You will have your sub amp set up with a low pass filter, so it will take the noise out.

You must have disturbed the head unit wiring in some way. How to sort it? Try taking it out and checking all the wiring again.

I have the same problem at the moment and can't seem to sort it. You can get ground loop isolators to go in the RCA lines. But to me thats curing the symptom not the cause. May be the only way though.