If I put multiple sets of armor on one mannequin, periodically, all but the pieces that are shown on the mannequin itself will disappear. This never happened in any of my Vanilla homes, but it has happened twice in the Falkreath homestead, once on the basemant mannequin and again on all the armory ones. I've heard people say that sometimes mannequins will duplicate armor, mine seem to be doing the opposite.

You sure you did not just take all the armour off and forget about it?