The CCD site offers the following advice that I urge you to follow:

My CD-Rom or CD-Writer does not work with CloneCD! CloneCD tells me, it is "not compatible"!

Most CD-ROMs and CD-Writers work fine with CloneCD. If you get a message that your CD-ROM is not compatible, please disable reading of Subchannel Data. Please make sure, that you use up-to-date drivers for your SCSI controller or the IDE controller on your motherboard. It is a good idea to use the IDE drivers that came with your operating system, because ALI, VIA or INTEL IDE drivers often cause problems. Please tell us, which device you are using. Use the "Send Email about a Device" form to send us an E-Mail. Probably we can support the device better in a future release.