What happened simply is the original return was processed and the missing payment is being requested which you know you will not owe once the amended return has processed. Since you should have sent the original balance due before you amended the return please look at the 1040X to see if line 16 is correct since the program assumes you made the original payment in full so if you didn't make the correction you actually may owe more once the amended return has been fully processed.
Look at the form 1040X …
Column A should have the figures from the original return, Column C the corrected figures and Column B the differences between the other 2 which needs an explanation on page 2 of the form 1040X.
If you completed it correctly you will see an entry on either line 16 OR 18:
On line 16 should be the amount you paid with your original return.
On line 18 should be the amount of your original refund you received.
Then you will see your extra refund on line 22 OR the new balance due you need to pay on line 20.
