If you run CP on more than 100 images, it will give an error “can’t write more than 2 digit string” and not complete the cycle. Given the presence of datasets of more than 100 images, this would be a great bug to fix.
As you can imagine, we run data sets with thousands of images without error. The bug you are mentioning, in the SaveImages module, happened when you try to have SaveImages automatically number each save as the cycle number (the N option). This error has been been corrected in the latest version. Please update, this should resolve your problems.