Confirmed as well. Only work around that I found was to empty a clip one at a time and move it into an ammo box, although having the ammo box in hand while emptying a clip would also cause either the ammo from the clip or one of the stacks in the ammo box to go to 0. From what i can see, if any other ammo of the same type is visible in the inventory screen (including in hand) one stack will always be set to 0.