If you have personal logistics unlocked, then you need to have a request for the ammo you want in logistic requests in order for auto-loader to refill your ammo.
This is done because there needs to be a way to signify when you don't want ammo refilled, so that you can un-equip the guns. The game doesn't allow players to remove their guns if there is ammo equipped, so if the mod insta-refills ammo then you can't remove the weapons (to fly on a space ship or upgrade to a different gun type).