Deluxe was 39.99 for a Federal return prior to March 1, when it increased to 59.99. All online paid online products increased in price on March 1 (actually the early season discounts expired, and the products returned to the undiscounted prices.)
If you recently saw a fee of 39.99, however, then that may be an extra service fee due to your payment method. Did you choose to pay the Deluxe fee out of your Federal refund? If so, that payment method has an additional 39.99 service fee (44.99 for California filers.)