Without changing any settings or making any updates, while trying to process orders (Sales > Orders > [View Order] > Invoice), Magento is no longer adding the shipping to the order. The "Order Grand Total" does not match the "Grand Total" directly below (see image below).
After the order is processed like this, there is an "Amount Due" left for shipping to be collected. I have looked everywhere and cannot find anyone having the same issue or a solution. Please help!