The federal cover letter should show the tax due for federal. Were you looking at the state cover letter? It also shows 4 quarterly estimated payments 1040ES slips for NEXT year. Those are optional to pay. Did you maybe just pay one of those? There is also a 1040-Voucher for the Tax Due. Did you send in the 1040-V voucher or just one of the 1040-ES slips? If you sent in a payment with a 1040ES slip it was applied to next year and not this year.
