I am not too familiar with how the sound is piped in game vs off audio CD. But if the audio CD is directly piped off the CD system while audio from game play is done through the rest of the hardware, maybe something isn't getting through clean?
Try plugging in a good headset or external speaker to CD's audio out jack and see if it sounds normal or bad. If it's normal, it may be in the connector from CD to the base or within the base system.
I'll stop rambling and let the real expert tackle this. :oops: