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I am not familiar with your head unit but I know some radios can control audio options for each source. My unit has adjustments for bass treble fade sub out etc in each source like radio, dvd, cd usb etc. I would check this first. For example, my radio can have the bass set to zero while the dvd can have the bass set to 5. If this is the case for your stereo, the sub out for the different sources can still be set to off.
What kind of car did you install this in? Did it have a factory radio in it? If I had to take a guess I would think that there is a factory amp that you may have hooked the blue wire from the alpine deck to. If this is the case when you switch to CD the alpine deck turns off the power to the power antenna lead(blue wire) and thus your factory amp. If this is the case hook the factory amp turn on to the blue and white wire and you should be good to go.