I made the mistake of running the program when prompted immediately after I installed it. Had the "delete errors" problem too. Right-clicked on the program icon from the start menu and opened as administrator. After that it worked like a charm.
I just wanted to give kudos to DV2 re: 'if you right-click on one of the files you are trying to delete, select "Open containing folder in explorer" and then try and delete the file manually.' After I did this, I still had to delete the checkmarked boxes the usual way through Duplicate Cleaner, but it worked!!