I've encountered a similar thing before. Your situation might be different, but the culprit on my end was actually SPID, or, more specifically, multiple SPID inis distributing outfits to the same NPCs.

Skyrim can't have more than one outfit for an NPC, so if something, for example SPID, distributes two to the NPC, things get funky and the NPC refuses to equip anything. Have a look through your SPID inis for ones that are distributing outfit records, see if that's causing it