If you call them, or write to them on this particular issue, you will likely not be able to deal with this.
Here is what needs to be done.
1. Verify how much tax was actually due; that is confirm that the return was properly prepared and the actual amount due was what the IRS says.
2. It would be nice to reveiew all the correspondenced you received from the IRS including the first notice telling you that you still owed 2004 taxes. In otherwards, for me it is valuable knowing, three figures: how much total was owed. How much you paid, and how much the IRS says you owed.
3. It is best to have representation to help you with this issue. You can pay for it by hiring a competent CPA or Tax attorney; but the IRS and the Fed has provided you with free assistance to help with these kinds of issues.
In order to know which free assistance you qualify for I need to know your filing status and adjusted gross income.
NOTE: since you did not have your SS number and did nto have the year of the return indicated, there is a hight possibility that the check in fact was mis-applied.