Timing is everything ... when you filed and when you made the payoff will be the key. Be aware that the IRS is a very large machine and the office that marks the account as paid, the time it takes for the debt indicator to be removed and/or any more penalties/interest are calculated up to the date of payment and the offices that process the return to issue the refund may not get the update timely. Eventually the IRS will figure out that they withheld too much of the refund and after any more interest/penalties were applied they will refund the excess ...note that this may take a few weeks to happen and there is really nothing you can do to speed things up.
