I have had numerous prepaid rates where the rates change after booking and payment is made. It shouldn't make any difference. You prepay the rate you have agreed. Same applies to any rates at which you reserve a room. Rates often go up or down after a booking is made, but the rate you book is the rate you pay. However, with non prepaid rates, you do have the choice of changing the rate if it goes down.
But the rate change shows on my profile and inside the reservation # confirmation folio. Not when I browse the same dates to check if the prices went up or down.
Just to double check, have your final rate ever changed under your reservation # folio?