@ralberts, if you currently have products which are out of stock and you used to have the setting Configuration > Stock > Subtract Stock: True, AND You had Configuration->Stock->Products status in Catalog when out of stock should be set to: 0, the products may be marked Out of Stock (as well as having Products Quantity set to 0).

You can check in admin->catalog->categories/products->(edit the product you want) and see if the Products Status is In Stock or Out of Stock.