I'm sure i've read that the STD changer is not that special.
I had trobles with mine, suffering similar symptoms. But I've changed my HU for an iPod ready one, and have since removed the changer, and put the extra storage box in it's place.
Don't think you're going to get any answers TBH, maybe a case of keeping a CD cleaning disc in the magazine, and running once a week or summit?!?