[Wonko The Sane]

I had this issue, myself, and the problem was the grounding as everyone else said... Although, I didn't buy anything extra to fix it.

I literally just pulled the deck out, started the car and played it while adding an additional chassis ground from the deck, I went and touched the chassis ground to a couple of different places/wires inside of the dash until I found one that gave me a solid connection, and my problem went away.

The issue is the noise sensitivity in the high-level to low-level adapter required to work with the stock amp. You're essentially taking your high-level signal from the speaker-out of the deck and running it through a filter to make it a low-level signal for the stock amp. ANY noise that happens in here will be amplified.

I know that this fixed it as shortly after that, I hit a bump and that wire came loose, and there was the unbearable whine again.

RCAs will not fix this.

Cheers!
~Aaron


Edit: I should clarify: The above is for an issue with an aftermarket stereo and the stock amp....

I had this issue with whine through my aftermarket amp later on, and it turned out that it was the noise isolation circuits in that MTX amp. I guess they really didn't plan on it being used for full-range, as it had no problem with it when the EQ was filtering out high range. I switched to a slightly higher quality Kicker amp and the problem went away. I did try to switch RCA cables first, as well as re-route the signal and speaker wires, but to no avail, swapping the amp was my only option there.