My hunch is it could be an input error on the IRS part, i.e. the client was given credit for someone else's estimated tax payment... I know this is rare but this did happen to me years ago.. a client mailed their return in and when the IRS inputted the schedule C income number on page 1 they accidentally inputted it on the capital gain line. They sent the client a refund check and said that I used the incorrect tax method, i.e. did not use the favorable capital gain tax rates... I had client return the refund check and eventually the i r s agreed with me...