Could you have possibly filed a mail-in return and your returns were never mailed to the IRS? Can you verify if your returns were e-filed and accepted by the IRS?
If you chose to file by mail within your tax return, then you would have needed to mail your return to the IRS.
If you e-filed, the IRS would receive it directly to either accept it or reject it. Either way, you would be notified.
This article will provide information on mailing a return.
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Did you mail or efile it? When? If you efiled was your return Accepted? When you efile you get back 2 emails. The first email only confirms the transmission. The second email says if the IRS (or state) Accepted or Rejected your efile. Just paying the fee doesn't file the return. After you paid did you continue on to the very end and hit the big orange Transmit Returns Now button?
When you log into your account you should also see the status and if it was Accepted or Rejected, Started, Printed, Ready to Mail, etc. What does it say?