What number are you using for your refund amount? You should be using the number as shown on the 1040 not the amount of the actual check. Example - if your original refund was $500 and then you amended and got an additional refund of $250, then your refund number is $750, not the $250. If that doesn't work, you may want to try your original refund of $500 in this scenario because the computer system may not be updated.
