Thanks to @VolvoGirl and @SteamTrain for your constructive skepticism. I followed your clues to find that I entered estimated taxes in two places – the correct place and also a form with a heading like "Other federal withholding." I've learned a lot here about how to check my work and also the risks of splitting the work with a spouse.
I might write a letter to the IRS asking if they'll waive the penalty (not the interest) – our first response to their letter was to think they made a mistake, and they initially wrote a letter accepting that explanation (and proof of estimated tax payments).
