If you have a CDJ-2000 and are using CDs then you're using them wrong. ;)
Just kidding.... That sounds like a weird problem. Have you tried burning a new CD to test if maybe there is a problem with the older dics? I have heard of burned CDs having priblems over time.
What kind of CD-R dics are you using? One rule which I heard many times before was that if the CD is the Green kind its good, Blue are bad. I am not sure if that's really true or not, though.