If the situation windytrail describes happens to someone else, look up "TAO", taxpayer advocate office, and take things up with them. They were created to help keep the IRS a bit more honest.
I received one of those postcard audits where the IRS claimed I owed them a nice sum, or hadn't done 1099-B correctly. I think I did a same day sale of stock, so the tax was already paid, but I needed to fill out 1099-B to show the cost basis and proceeds were about the same. Naturally the IRS assumed it was fresh money they could tax. So in that case, I filed 1040-X, to amend my return, and that shut them up.
If you filed by hand, after double checking for accounts you missed, you could buy tax software and run the numbers through there. If their numbers were slightly different but better than the IRS conclusion, you could file 1040-X with the tax software (might require mailing?), and let the IRS respond to that.
Finally, many years ago I downloaded my tax records from the IRS itself. Very, very educational. They round off every dollar amount, which I didn't know until I saw it for myself. I assume if I follow their method my taxes will come out more like their calculations. But you might be able to use that same mechanism to find out what income they think you owe, and compare it to what you calculated.
And for me, I found it interesting to read several books on IRS audits. Might not be for everyone, but I got the worst audit of all... not the ones asking for money about one area... a "survey audit", where they look at every single form in your taxes just to see what taxpayers are doing. It's much more involved, and requires sitting with an IRS auditor going over your taxes. Luckily no problems for me, so maybe I made the rest of the taxpayers look better by being part of their survey, many years ago.