I'm telling on myself by saying this, felt kinda stupid when it happened but was funny after I figured it out. When I was on my maiden ride on my new bike, my first with navigation, I was about ready to turn around and head back to the dealer because the speakers kept cutting out. Had an epiphany when I got home and realized it was the navigation system trying to talk to me but the speaker switch wasn't in the proper position to allow the audio to come through, it would interrupt the stereo though. In your case it sounds more like a wire connection issue if just one side is affected but is odd that it's more noticeable with a CD. Maybe you crank up your favorites more than the radio so you notice it more? Definitely have them take a look at it, hopefully it will behave the same for the service tech.