Leanord at ARC did tell me that the Phillips transport used in the CD2 adheres very closely to the Red Book standard.Which means anything that doesn't comply with the standard will have some trouble. If the disc has flaws it won't track. What Weiserb and Whatjd said is correct from my experience. Both a friend of mine and I owned CD1's and would track anything! We both have CD2's now and do find them to be more fussy about what you play(that being said I have next to no problem with this, he on the other hand buys a lot more rare and used CD's).
To address Tswhitsel's feelings about build quality, yes the CD1 and the CD2 use a standard(read plastic)phillips transport. Aside from that, the thing is wonderfuly well made, "like a tank", the board inside is a work of art, and you need to spend mucho more to get a better constructed player, something like a Wadia 860 or the new CD3, which you can't buy new for $3K or used for around $1500!
Try cleaning or polishing some of the discs that skip with something made for that pourpose and it can't hurt to call ARC and talk to them about it. You may just have a fiber of some sort floating around in there. Do you have a cat?