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I don't have experience with dealing with the IRS beyond submitting tax returns, so I'd like some advice on how to proceed this time.

I've been a 'pencil'-paper tax filer, so as usual I used Free Fillable forms via the IRS site to file our MJF 2010 taxes. But before sending it off, I also used Turbo Tax online to see whether I'll get the same result and I did. Well, the refund that was deposited into our checking account was $100+ less than on the 1040. Two weeks later on Saturday we received a letter from the IRS with explanation and now I know why.

It's because of the qualified dividends. For some reason, the IRS calculated our tax strictly on the taxable income though I showed our ordinary and qualified dividends on 9a and 9b lines, respectively, on the 1040 and also submitted Schedule B. So, the IRS decided not to apply favorable dividend treatment to us :(.

What should I do now? If it was less than $50, maybe I'd leave it alone, but now I'd like to get the rest of the refund.

Should I call or should I mail-in? If by mail, what should I send?
Should I type a letter explaining in words or just make a copy of my Line 44 (Tax) calculation in the 1040 instructions and send back?
Do I have to include another copy of 1040?

Thank you very much.

PS. I hope the above occurred not due to the order of forms on the Free Fillable site, because I couldn't rearrange them in the correct sequence there. So, it was something like this: 1040, W-2, Schedule B, 2441, W-2, Schedule D, etc.
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