ADDENDUM:
Also, since it has been so long, had you tried previously to speak to the IRS about this? i.e., is there more to the story? Had you gotten any letters about delays, etc.?
You might try phoning the IRS Taxpayer Advocate Service. Since they are present in each state, they might still be taking calls at your local taxpayer advocate service, but I'm not sure.
At the following IRS website, find the USA map and click on your state, and it will give you the number of your IRS Taxpayer Advocate.
https://taxpayeradvocate.irs.gov/contact-us
Also see this article for more info on how the Taxpayer Advocate Service works::
http://www.irs.gov/taxtopics/tc104.html
