If you saw the $900 credit, you likely were in the 1040X and attempting to amend. This is the most common thing that happens after you file the first time. Did you print and mail the return? If it was the 1040X you look at line 13 column A you should see the original amount you paid, then line B would have been the net change with line C being the amount that you should have actually paid.
Your 1040 line 37 would show the $1,000 you paid.
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