Last week I received a 'Notice of Additional Tax Due' from New York State stating that I failed to report Federal audit changes to them. This was for the tax year 2010 and stated I owe an additional $211.
Of course I didn't remember any audit changes and pulled all my records for that tax year. Surprise! I found a notice from the IRS dated 2/14/2012 that I owed an additional $625 (plus interest) because I understated my wife's gambling winnings by $2,500. We paid the additional tax at the time but for some reason I neglected to dig deeper into our records.

A little background:
The reason for the understatement was because my wife had received two receipts from the NYS lottery for $2,500 in winnings. Each receipt was the same date, same amount and except for one digit in the receipt number, identical in every respect. At the time, I thought one was a copy for my records and only reported $2,500 plus $1,300 in slot winnings from Caesars in Atlantic City.
We itemized our deductions for that year and she had gambling losses exceeding her winnings (I have a win/loss statement for that year from Caesars).
We never should have paid the additional taxes because her losses still exceeded her winnings even with the additional $2,500.

The question:
Is there any way I can have the IRS refund the extra $625 we paid in error and do I have to pay the additional money New York State says we owe them?

Thank you in advance for your help.

If you overpaid on your taxes for a certain tax year, you have not lost the money forever. you need to alert the IRS by correcting your tax return; but it may take time to process.UNLESS you are audited, IRS won't give you a refund unless and until you ask for it. Since you were audited, it is possible for the IRS to discover the error and give you a "rebate," which is different from a refund. A rebate results from a re-calculation of your tax by the IRS showing that you paid too much tax AS YOU ACTUALLY OVERPAID TAXES; you may go to a professional tax preparer, an IRS EA/a CPA and have them examine your records to determine if you did in fact overpay. If you did, they can help you file form 1040X to get a return of your excessive payment. Under the federal tax code, a taxpayer has 3 years from the filing date of the relevant tax return in which to file an amended return. For example, if the original due date was April 15, 2011 (for tax year 2010), the taxpayer would have three years, until April 15, 2014, to file a tax return and claim a refund. The statute of limitations may be extended if the taxpayer filed an extension to extend the original tax return deadline.

I have already prepared a 1040X to send in however if I am limited to 3 years after the filing date, it looks loke I'm too late or is it 3 years from the date of the CP2000 notice wich was 2/27/2012?

no; You generally must file an amended return within three years of the date you filed the original return or within two years after the date you paid the tax, whichever is later.

So basically you're saying I have no chance of getting a credit or a refund for the additional tax I paid to the IRS and I need to pay the additional tax to NY State.

As said, if you are beyond the three-year period, then, you can only receive refunds for overpaid taxes that were actually paid during the previous two years.When a refund has expired, that refund money is kept by the federal government. In IRS terminology, an expired refund is considered an "excess collection". That refund money cannot be sent to the taxpayer as a check. Nor can the refund money be applied as a payment towards another tax year for which a person might still owe the government. Nor can be refund be applied to another year as an estimated payment.



NYS also provides statutes of limitations for the assessment and collection of taxes. you need to contact the dept of finance of NYS for more info on your issue.
Statutes of limitation for state tax returns vary by state. For example, in CA the statute of limitations for making state assessments is four years from the date of filing. However, if the IRS adjusts your tax return, no statute of limitations bars CA from assessing additional taxes that you owe.