Uncheck all the things the red arrows are pointing to in the ORGANIZER preference file. All the thingds are in the media analysis tab.

I've never really understood users being so focused on duplicate photos. I've got copies of copies and backups of various images- I think It's a mistake to only have one copy of an image- What if the HDD the image is one goes bad? No worries, just go to the other copy on the other hard drive.
Who cares if there are 10 copies of a photo of aunt edna strapped to the roof of the station wagon? Not me. OMG I have 10 copies of that one photo- so? "Hey Bill, I noticed you have 5 copies of that Aunt Edna photo" "Yeah, so what?"
"But I gotta save space"-- What for? If you arerunning out of space yo uare doing something wrong.
"I gotta keep my organizer organzied"- You do reallize no one in your family cares about your Organizer?
"I gotta keep track of my picutres of aunt edna"-- and do what with them?