I had this problem last week and am waiting on another order at the moment. I called Performance and they asked me to fax them my confirmation email showing that the cupon code gave the discount and that they would refund the difference. I hope to not have to do this every time but for 20% am willing to.

Edit: Just checked and they actually refunded extra. Also the order I was waiting for today came in and the 20% discount was billed properly.