For some users, when deleting duplicate tracks in Tune Sweeper, iTunes shows a dialogue box asking if you would like to delete a track for every duplication that Tune Sweeper has found.
This will halt the duplicate removal process, and can be very annoying to keep having to allow the removal of each duplicate.
Signing out of your iTunes account in iTunes before using Tune Sweeper will prevent you from experiencing this issue.
On a PC - you can access the iTunes menus by tapping the Alt key on your keyboard.