Paying the fees does not file the return or guarantee it is Accepted. You had to continue on and hit the big orange Transmit Returns Now button. If you did efile then maybe it Rejected.
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.
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?
