For some reason my items stopped auto-stacking recently, and now the only way to get single stack-able items to stack, is to use the inventory Sort:Auto|Manual menu buttons.
EDIT/UPDATE: Setting the menu config 'Inventory Sort' to 'Auto' seems to force items to stack, but my items would stack (without this set) previously for years, so I'm not sure why it stopped now. Is this normal behavior (to only stack when inventory sort is set to auto)?