I have downloaded the latest code, and the gift certificates do not seem to be updating after a successful completed purchase using them. Checked the database, my $10 gift cert that I used to successfully complete a $2.99 zero-total purchase with, still shows a 10.00 value in uc_gift_certificates table.

Also in the invoice (emailed and through Order History), the token [order-payment-method] is not being replaced correctly.

Finally, and this is minor, the Gift Certificates line item comes after the Subtotal in the Order Detail screen. Since it's a subtraction, it should probably come after the Subtotal.