Sometimes I have trouble with Clone DVD 2; when I am actually using it to burn the DVD it occasionally acts up and gives me the same message. You know how there are three options on Clone DVD 2? Try the one that just creates a new DVD video file, not the one that writes it too. Once you have created a new (and shrunk) DVD file, you should be able to burn it using the writer option on Clone DVD 2 or some other writing program (if you own one).
Also...DVD Shrink is a freeware program that will do the job as well, but it will not do the burning all by itself like Clone DVD 2 does. Good luck.
Phil in CA