I can't be sure from your description, but it sounds like you ran afoul of the option in the 2210 to annualize your income to see if you can avoid an underpayment penalty.
As you can imagine, you can't wait until the 4th quarter to pay the 90% of your tax, because US taxes are a "pay-as-you-go" system.
Instead, the 2210 processing allows you to enter how much income you had per quarter and then it annualizes the income to see if you paid an appropriate amount of tax for the quarter, based on your income up to that point.
So it can happen that you have an estimated tax underpayment for one quarter even if you ended up paying more than the amount due by the end of the year.
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