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I love FEX. So, this is in no way shape or form to become a rant of any sort. What I'm about to say might boggle the minds of some of you. However, I am hoping to help some others.
I found that FEX saw duplicates of some of my fonts when I know darn well there weren't any. In a last bit of desperation I tried activating the family. Well, of course, it saw some as already active, but when I skipped all the rest of the messages it still ends up with a complete set of active fonts. I can make it happen with the Helvetica family:
So after activating them, I simply selected those activated fonts, dragged them out (exported them), removed the font from FEX, cleaned the manage folder, quit FEX, emptied the trash, restarted FEX, and imported the newly created set from the desktop. All is right with the world now.