From my inventory, I will log out and log in later and my ammo box is gone. I always make sure to pick it back up if I have to put it down to view all of the inventory slots, so it's not a case of me simply dropping it and forgetting to pick it up.

On that note, ammo boxes should allow you to view all ammo inside without having to put it on the ground, especially with the issues of missing loot and objects falling through the world.