it could be alternator noise. Make sure your audio wires arn't running parrallel with the power wires, but this is a bigger problem if you have an external amp powering the speakers.
there could be an auto-volume function on the cd player, too :dunno: I'm not too familiar with that model pioneer HU, but I do know that pioneer loves to throw gimicks into their products. If you don't have an external amp, look into one. HU's don't produce enough power to make your interior speakers sound their optimum. however, pioneer isn't exactly the greatest manufacture out there, either.