I'm also experiencing this problem. It's not so bad with regular looting because the window closes as soon as you move, but it makes disenchanting really annoying because the disenchanting loot window stays open until you log out of the game. Even if you reload the UI, the disenchanting window is there but invisible and prevents any further disenchanting until you log out.
Edit: This seems to have stopped happening with quest items, but regular loot still is displaying in the loot window even after looting it.