OK! I found the problem!
In the save you sent me, you are using Ammo Loader storage chests to hold the ammo. In the mod, the storage chests (as opposed to all other chest types) have a special function. Instead of distributing items put into them, they are receptacles the mod can use to store ammo/fuel when upgrading or returning items from entities. They do not work as distributors of items.
Simply replace the Storage chests with Ammo Loader base chests or Ammo Loader requester/passive provider chests, and the problem should disappear.
I do see how this could be confusing however. I think to make this more clear, I may remove the number that appears over the storage chests to indicate that it is not eligible to link to entity inventories.
Let me know if you still have problems after implementing this solution!