You mean naked as in "When I drag the clothing on the characters in the editor, the characters appear dressed, but when I start the game they're not wearing any armour"?
If that's the case, the solution is giving each character the appropriate feat so they can use light/medium/heavy armour. The latest patch helps prevent this by informing you when characters can't use a particular item you're trying to equip, but doesn't solve conflicts already there. Try giving them the right feats, that should do the trick.
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