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The IRS will correct certain items during the processing of your tax return, for example, if you made a math error or entered the wrong withholding amount from your W-2. You should have received a notice explaining the correction. Sometimes especially if you received your refund by direct deposit, the IRS notice explaining the difference will arrive in the mail a few days later.
IRS advises that "if you receive a refund to for an amount that is more than you expected, do not cash the check until you receive a notice explaining the difference. Follow the instructions on the notice."
If you do not receive a notice from IRS by the end of the week, I would advise you to call their 1-800-829-1040 help line to ask about the refund difference and that you elected the refund to applied to your 2010 estimated tax. If you still want the overpayment applied to 2010, you will have to send back the refund check to IRS and write "void" on the back of it with a note that this credit should have been applied to your 2010 account. If you want the "extra" amount they added refunded to you, they can issue you a corrected refund check after you send back the original but it may take up to 8 weeks.
Hope this helps,