Hi @johnjohn1003,
Thank you for the screenshots. I’m afraid that putting negative values in the Cost per order column is not the proper way of applying the discounts and, in fact, the negative shipping cost value shouldn’t affect the cart total since they are two different parameters. The fact it was working previously was reported to WooCommerce authors as a bug. Once such rule is added now, it’s substracting the set value from the shipping cost, even when it reaches 0, substracting should be stopped and the shipping should be free. If the shipping cost amount is 0, it still substracts the negative value coming from the rule, but from the cart total this time, lowering the order value. At this moment the same problem happens if the WooCommerce Flat rate is used. That’s why we believe it will be fixed in the upcoming WooCommerce updates.
However, we highly advise not to use the shipping cost calculation rules to apply the discounts reffering to order total, otherwise they may interfere with the other calculation mechanisms and may cause further malfunctioning. In your case I believe it would be much safer to use some additional plugin to apply the discount directly to order total instead of substracting it from the shipping.