One thing I noticed in installing other imaging programs is that some create duplicates (thumbnails presumably) in the "Pictures" directory. For instance, the program Luminar does this within Pictures>Luminar 4 Catalog. So if you have been trialing other programs, this could be part of the duplicates issue. As Tomasc pointed out, try to see where these images are being stored and what attributes they have as that may provide a clue.
In terms of getting rid of the duplicates, I wonder if you could use another program outside of PhotoDirector to do that, then rescan / resync the folders within PhotoDirector.