If you read my answer above those are a list of possible reasons, not the actual reason. The amount you claimed on 1040 line 30 is wrong so they took it off your return. They either reduced your refund or now you owe more.
You seem to know you missed entering a payment you got. So you tried to get it again on line 30. How much was on line 30? You do owe it back. You don't need to amend. Just pay the tax due. There is nothing you can change or fix.
