I've noticed that any item I've found... must be saved at a save point. If I'm killed by our Rat Oppressors... the item disappears. It isn't at the place I originally found it... nor is it anywhere else I've looked. Nowhere to be found. Only when I start a completely new game can I find the item. (Thief Boots, Pirate Hat etc.)
Also.... II can't get the Galley Chest Key... the Rat guarding the chest won't drop it. I've knocked him senseless three times but no key on his dazed body.