Yeah thats what I was goin to say I think it has something to do with the ground, and with your stereo, I know one thing its annoying as hell, been in a few cars like that.
Check your grounds...especially at the amp. Try this. Unplug your RCA's to your amp then see if the wine is still there, if not then the whine is coming from the amp....check your ground and how the RCA's are ran. Don't run your power wire with your rca's...you get noise. If after unhooking the RCA's the whine is still there then rehook them back up at the amp and unplug them at the deck and check again. Just keep unhooking things untill you find it. How were the wires ran in the car? Where is your ground for the amp? How about the ground for other items in the car? There are so many ways that engine noise can get into a car is almost insane trying to track it down. Good luck.