So based on the part number, i'm assuming you have the none cd version of that pioneer?
so the sub works when the tuner radio is activated via source menu but not when apple ipod is inserted!?
Have you tried the average usb flash drive with mp3 file on it? try that as a process of ellimination and if that works then we know that the problem lies in perhaps a compatibility issue with the ipod your using although it should support ipod touch and iphone models of today. earlier generation ipods are questionable.
Maybe try the USB idea and this will perhaps give you a better idea as to whether the unit is at fault. Although if your still getting sound out from ordinary speaker outputs when in usb mode then that is a bizzarre issue. crank up the volume to see if your getting even an ounce of sound from the sub when ipod is playing. Could be an on board amplifier issue within the pioneer. Some of the USB's have known to fail for unknown reason. Sorry if I cant be of any more help.
