I concur turn your gains down.

 

What kind of amp/head unit?

 

1) No I am not listening to the radio, just CD's

2) The speakers are connected to an amp

3) Today I just noticed that if I listen VERY carefully, I can hear some alternator whine, very slight, but still there

So I will do some further diagnosis and let you know what I find.

 

Also, if it were due to the fact that the gains were set too high, which they aren't because they are ALL the way down(set at 8 volts input), that doesn't explain why there's no noise at all when the car is off, right?

I just don't see how a car running or not would make any difference to indicate improperly set gains. If the gains are set incorrectly, this will show regardless of whether the engine is running or not...