Same problem occurs with Group Discounts. Run the order with no discount, add the customer to a discount group, edit the order - the total is wrong.

Group Discount include tax = false, include shipping = false, recalculate tax = standard.

Original Order:
Sub-Total $500
FL Tax 7% 35.00
Total $535.00


Add Group discount of 25%:

Sub-Total $500
Group Discount $125
FL Tax 7% 26.25
Total $392.50

should be $401.25.