I only use CloneDVD to 'read' the DVD (I also have 'AnyDVD' running) but I use 'Nero' to write the new DVD. I find this to be the best combination. Sure you have to purchase the above mentioned programs but it never fails for me.
I too have had some problems and errors using CloneDVD to do the writing.
Using CloneDVD, when the reading stops and the little message comes up to insert the blank media, just choose cancel. To do it this way you 'must' untick the box in CloneDVD which says something like "Delete files after successful copy". You dont want to delete the files! After the reading just open Nero and choose "write DVD movie files". Works every time!