i can't say exactly, but the wires are (probably) unshielded so any radio interference will mess with the speakers producing sounds.
i couldn't keep my old iPhone / 3Gs in the cubby because when it would jump to the EDGE network my speakers made some funky noises even if the stereo was off.
do you have the rear speakers?
probably electrical interference by the alternator, not the engine...
of course i could be talking out of my a$$ and be totally wrong.
my '88 ford tempo did the same thing
http://www.sacskyranch.com/altnoise.htm