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Unfortunately, if the return was filed after the filing extension deadline, the refund statute runs from the original due date of the return without regard to extensions. Since a return was not filed by the extended filing date, the extension is disregarded for the refund statute. Therefore, the return would have needed to be filed by 4/15/2009 to obtain a refund. If you had filed a return by 10/15/2006, you would have had until 10/15/2009 to AMEND if you wanted to claim another refund. There is no way to appeal this statute rule.
See IRC 6511, http://www.law.cornell.edu/uscode/html/uscode26/usc_sec_26_00006511----000-.html
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