I was having the same problem. At first I thought this was a problem with AnyDVD, but I think it may be a porblem with CloneDVD or AnyDVD or both? (I am running Windows 2000 PRO).
After several attempts to uninstall and reinstall the software, defrag, clean registry, etc. I could only fix the problem with a format of my hard drive, reinstall of the OS and a reinstall of PREVIOUS versions of Clone and Any (that's CLONE 22.214.171.124 from Feb 2006 and AnyDVD 126.96.36.199 from April 12, 2006. Fortunately, I had saved these to a CD. As you know you can't download old versions from the Slysoft site. I really disagree with this policy. If someone has a problem with a new release there's no way to download a version you know worked on your system?? Bad Slysoft.. Bad!! ; )
You should know that after the format and reinstall of my OS, I did try to reinstall the newest versions of AnyDVD and CloneDVD, but my system crashed! Only uninstalling these versions and reinstalling CloneDVD 188.8.131.52 and AnyDVD 184.108.40.206 solved the problem.
What OS are you using? Is it 98, 2000 or XP?
Hope this helps!