Three year deadline to file and receive a refund.

I received a refund for my 2002 taxes, which were filed in May 2006. The accountant said that the IRS probably would not issue this refund, since it was more than three years past the filing deadline of April 15th 2006, but they did issue it. TurboTax states: "If you are due a refund (meaning you have overpaid your tax), you can wait up to three years from the original April 15 deadline to file your return and claim your refund." However other statements on this subject that I found seem to indicate that if you file an extension then the three years starts when the extension ends. When does the three year limit actually start? Does it start on April 15th, or if you filed an extension does it start at the end of the extension? The fact that I got a refund seems to indicate that the three years starts at the end of the extension, or was I just lucky? The refund was for around $5000.