Yes, unfortunately you are in the same boat. When you originally filed with the refund transfer option, the bank account number that was passed to the IRS was the number for the temporary account that was going to be opened in your name to receive the refund. Even though your tax return was delayed and you had to pay separately, that is still the only bank information the IRS has for you, unless you went on the IRS website over the summer and corrected your bank information.
