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A year later I finally figured out what happened after requesting a tax transcript. I compared the transcript to my copy of the return and found a discrepancy which explains the check I received. I never did receive a letter with an explanation, just a check.

I received a state tax refund from the prior year and included it in my 2011 income (line 10 on form 1040). The transcript did not include this income: it showed $0 on line 10. My CPA filed the taxes electronically and somehow what he submitted didn't match what the IRS received (everything else on the transcript matched). Must have been a bug in his tax software.

Anyway the IRS calculated tax due (based on the information they had) and compared that to what I paid and sent a check for the difference (which matched exactly to the line 10 discrepancy). This must have been done by some automated process.

I think I"m going to file an amended return, although I have not yet been audited, the IRS incorrectly issued me a refund.
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