First step I'd take is to look up your IRS transcripts. See if the payment has posted, and whether a balance still exists. Any tax professional can do that for you, but you can do it yourself here: http://www.irs.gov/Individuals/Get-Transcript
Almost all IRS letters are generated by computers, and mistakes are made/correspondence crosses in the mail. After you obtain transcripts for the tax year(s) in question, give them a call at (800) 829-1040 and find out what's going on. One thing I will unequivocally recommend is to stay calm with the IRS rep and don't take it personally. If this strategy doesn't work, consider speaking to a licensed tax professional.
For what it's worth, the IRS just added a function that allows you to pay online through the IRS website: http://www.irs.gov/Payments/Direct-Pay. Pay1040 and similar sites have always seemed a bit questionable to me, especially when you consider that EFTPS.gov is available. Adding a third party to the equation creates an unnecessary possibility of error, IMO.
Robert Hoffman is a tax attorney licensed in California. The information presented here is general in nature and is not intended as a substitute for legal advice. This posting does not create any attorney-client relationship with the author. For competent advice about your particular situation, consult your own attorney.
Contact the Taxpayer Advocate at the IRS. They should be able to help you correct this matter. If they cannot, an Enrolled Agent or Taxpreparer may be able to help you. If all eles fails, contact your congressman and if that doesn't work, you will need to hire a Tax attorney; however, with the proof you have it should be done at the first level.
Every thing that I am saying here is my opinion and it is not based on any particular case. My response is just unsupported general information. If it helps you to resolve an issue that's great but do not rely on it as legal advice because it is not based on the facts in your case and it is not based on any specific legal research. Answering this question creates no relationship between the writer and reader of the writing. I am not your attorney now, nor have I been on the past.
I agree with my colleagues. I would add that I have dealt with this problem before - occasionally the IRS will post a taxpayer's funds to the wrong account. Its a pain in the _____ to get them to fix it. Try contacting the taxpayer advocate for self help. http://www.irs.gov/Advocate Or you could hire someone to take care of it for you... A professional could probably dispatch the problem with a call (or several) to the IRS tax practitioner hotline.