Thanks for your question.
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
Hope this helps,