I don't know about subcategories, but family parameters tend to do this quite often. That's the main reason behind shared parameters - to ensure a custom parameter is EXACTLY the same between various families and projects, such that slight differences do not cause these duplicates.

As for sub categories, I'd have thought the name is the only key for equality checks. Are you sure those names are the exact same length and characters? Note you do get unicode chars which are slightly different (though may look the same). E.g. U+00A0 is the normal (Non-breaking Space), but U+2003 (Em Space - looks the same) though Revit sees it as a different character. For this reason (and due to parameters in formulas) I prefer not to use spaces and strange chars in names. It gets too easy to have non-apparent differences.

Linked model perhaps?

Well, that's a possibility, but the same thing occurred with our subcategory "Worksurface" which doesn't contain any spaces.

No, definitely not a linked model. Just families loaded into the project.

What happens when you place them in a new project file? Have you narrowed it down to a few specific families or is it the whole library category of your custom stuff? Are there nested families in them (shared/not-shared)?

Sorry, thought I deleted my post....realized it couldn't be a linked model later...

Unless they are shared vs a family parameter....not a clue

(Saw a tweet about a shared parameter and family parameter being identical....and a caption of "Your Welcome"...)