Sounds like the payment did not get to the IRS correctly ... either you mailed it to the wrong address or the payment was mailed with the return and it did not get properly deposited.
In this case I would pay the bill they mailed you and put a stop payment on the original check with your bank so if it gets found they cannot cash it. As for any late payment penalty you may be able to get it waived by sending in a copy of the check if you have a carbon duplicate plus the stop payment order from the bank. Sadly the interest cannot be waived.
Next time have the payment direct debited or pay the feds directly online so you have a receipt and instant confirmation of payment.
