I'm receiving "files were not processed as they are Protected", however, I don't understand why Duplicate Cleaner is calling the files "protected". They are not marked read-only and are just regular files on an external USB drive.
They might be in your Windows or Program Files folders - there's an option to protect these too. I wouldn't use DC to delete stuff from these folders though.
Deleting these files is a valid operation - I've reloaded Win XP a couple of times and have just upgraded in place to Win7. Each time, a Windows.old is created, containing copies of My documents and Program Files among other things. I'm quite happy to keep a single copy of these apparently redundant files, but I now have 5 copies and my disk is getting full. I got DUplicate Cleaner specifically to help me with this problem, and it still won't delete them, even when run in Administrator mode. Is there an override?