Have you called the IRS to discuss the issue?
Is the IRS saying you never paid the money? Or, is it saying you paid it late (i.e., after the due date)?
Under the "mail box rule," if you mail your return/check no later than April 15th, and the IRS receives it after April 15th, the date you mailed the return/check is generally the date that it is treated as received by the IRS. See 26 USC 7502(a).
If the IRS is merely saying it never received payment, but you have the canceled check for the amount due, it should be pretty easy to make this go away. You may have to write a short letter to the IRS and include a copy of the canceled check. If it is something else, it may be a little more difficult. Make sure you keep notes of any discussion with the IRS (names, dates, stuff discussed) and also keep copies of anything you send to the IRS to get this resolved. Sometimes it takes more than one letter.
As one of the other posters said, it is always a good idea to send anything to the IRS by certified mail with return receipt requested.
Please email me if you have more questions. Good luck mate.