When you board a ship, you have to be very careful looting corpses. Leaving aside your men losing the fight - if you loot a corpse when the lock icon is on screen teeling you to enter the enemy captains cabin, you cant get it back. I looted about ten corpses, 6 cupboards, over multiple saves - and got a huge haul of gold, diamonds, rings, weapons - but had to load the prebattle save so I could get at the enemy captain and exit the scene