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Irs says I didn't file I did!

I have several questions.  First, I received notification that I owed the IRS money for failing to file in 2003.  I sent in all the paperwork, but still ended up in an audit, in which they said that I owed $2300, but since I had paid in $5500, no additional monies were owed.  However, since the audit was in 2009, and the taxes were paid in 2003, they are claiming they do not have to pay me back the additional monies because of the 3 year statute of limitations for filing and receipt of funds.  I do not agree with this, as I did everything, including showing them a copy of the envelope I sent.  Is this accurate?  I have a tax guy that told me that since they didn't add settlement charges for failing to file (from the audit), that statute shouldn't apply.  Any guidance (reference,  please) on this?

Second, I had several years where I did not file because I did not make enough money...but I still had mortgage interest and real estate taxes that I paid.  Can I go back and refile in order to use these annual deductions to form a NOL to carry forward or backward?

Lastly, since the screwup with the 2003 taxes, the IRS has withheld refunds from other years..when should I expect them to release the funds, and should I expect interest on the monies that should have been paid?

Thanks.

 

Gary G.

 

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