It sounds like you’re using the Pro version of System Ninja, so you will get a faster response if you go through the priority support page instead of the forum.
In Pro, the “one-click” cleaning screen automatically deletes all files found – unless System Ninja isn’t completely sure, in which case you get a warning.
Repair corrects a small number of known issues with Windows, such as corrupted thumbnails, misconfigured HOSTS file, etc. For the overwhelming majority of users, it will not find anything.