PittsTake

I seem to be running into a problem that doesn't make sense. I have a quern, attached to a windmill. If I fill the storage box that feeds the quern, and then go about my business, the quern empties the chest, but I only get a few of the items. This time it was a full load of chalk stone, and I got a single stack of ground chalk. This seems to be a game breaking bug, but I can't find anything addressing it. Do I need to waste my time manually grinding things, because honestly that will probably drive me away from what is otherwise an enjoyable game.