It sounds to me like your problem is simply a defective CD with data destroyed in some places beyond the capability of the error correction circuits to cope with. This will cause a crackling sound. Try the CD(s) on a different system, if the problem still occurs, the CD is at fault. If the problem only shows up on your system, then your CD transport is probably not handling errors well.
If the problem shows up worse on the first tracks on the CD, then it likely is a combination of a defective CD and inadequate transport performance.
The CD is read from inside to outside (the opposite of a record) and spins much faster on the first tracks, making read errors more likely on the early tracks. An out of round, not flat, or slightly damaged CD can cause problems on one transport, and play just fine on another, depending upon the transport's error correction capability.
Frank Van Alstine