I vaguely recall seeing those myself. If I remember, when Shrink is prcoessing files to be written, it stores files in a temp directory that you specify. When you go to make the second copy, Shrink wants to go through the whole process again, but can't because it alreadys 'sees' processed files.
The simple solution to your problem is to build ISO images. That way you can make more than one copy. As an alternate you could specify different folders for each job, but does one really want to go through that hassle?