Well, I have to report that at last I've solved the mystery of 'protected' dupe files not being deleted. More's the point, I could have solved this months ago had I merely looked in 'options', so silly me!
In my case I had a sub directories for downloaded files off the main program dirs in C:\Program files. As C:\program files was ticked as protected, the files could not be deleted. Simple! A work around is simple. Either unprotect C:\program files or simply point any downloads to a different directory.
Summary... Buggerall wrong with Duplicate Cleaner. Works a treat.