Hi! I have something similar. If a weapon is equipped without ammo, or when you take the equipped ammo in your hand, the worker chest will gradually empty. Even if you have no turrets or vehicles standing around.
Edit: Only when I put the ammunition I hold in my hand somewhere, the 10 rounds are filled up and the disappearance stops. As if he wants to fill the slot, but since the hand is in use, the ammunition falls beside it. A time delay might help there, like 10 seconds waiting time, maybe as a option to switch on/off and then the slot is tried to fill up. (Could even be disguised as a reload feature :D ...whereby that does not sound so uninteresting at all, by turrets, stopp shooting, 3 sec about the reloading and with the player a few seconds more.) In that time, you've already put down the ammo.
Ok, I'll just take half of the ammo (right click) and put it somewhere, but if you don't know that, some ammo can disappear, if this should generally be the case.