My son just had a friend from Best Buy install (2) 12 inch subs in his car. He also installed a dedicated sub amplifier to drive the subs. The amp/subs only respond to the tuner, but immediately shut off (or just don't work) when the cd button is pushed. What's up with that?
not sure, more information would be helpful... kinda sounds like the head unit is the problem, try messing with settings in the cd mode, sometimes the settings differ in different modes.