Since you can see the Tax Withheld Smart worksheet on the Form 2210, I'll assume you are using desktop software. As you'll see on that worksheet, if you also had any estimated tax payments in addition to withholding, there's a warning there to be sure you don't enter them in one of the columns of the Tax Withheld Smart worksheet. Estimates paid, if any, are entered in another place in the program. So I'll assume from what you wrote above that you are only entering withholding in the Tax Withheld Smart worksheet, as instructed on the form.
If it was me, and if I was trying to troubleshoot, one of the first places I'd look is a TurboTax worksheet called Tax Payments, which shows all tax payments of every variety and see if it all correlates with the 2210. Go into Forms Mode and in the left column list of forms, scroll down to one called Tax Payments. Is there any clue there as to what might be happening? Does the total amount of Federal withholding shown there on the Tax Payments worksheet equal the total of the 4 columns of your Tax Withheld Smart worksheet of the 2210?
