No idea, but thanks for posting this question. I had been waiting for the Tax Withholding Estimator to come back online and it still has the Outage banner so I had been assuming that it was still down. More on reddit.com

https://www.irs.gov/pub/irs-pdf/p15t.pdf More on reddit.com

One of the common reasons that married couples find they've underpaid is that one or both of them filled out W-4, indicated in Step 1 "Married Filing Jointly" but then did not make the adjustment in Step 2(c) of checking a box to indicate spouse also has income. If you don't do that or make some other adjustment, what happens is each job thinks its the only income source for the couple, so each job assumes the yearly income can fill the full Married standard deduction and the full size Married tax brackets. This ends up underpaying because it acts sort of as if your tax brackets are twice as "roomy" as they really are. What checking the Step 2(c) box does is have each job instead treat the income as if it's filling up half the Married standard deduction and tax brackets half the size of the Married tax brackets, which can end up doing withholding more accurately, especially if you together just have two jobs, your incomes are not in widely disparate tax brackets, and your income is not too variable. In many cases, having both spouses check Step 2(c) box is enough to get withholding to be better. So I'd first look at your W-4 settings (if you kept a copy of what you handed in) and see if Step 2(c) box was unchecked. Or if you elect settings online, look for something about multiple incomes. If you want to use the online withholding calculator, unfortunately what it does is a bit murky, but it does NOT have you both check step 2(c). It makes a suggestion that leaves Step 2(c) unchecked, figures what amount of withholding would happen based on that (which will be too low), then to force the withholding to be appropriate for the income you've told it you will have, it typically would make a suggestion for Step 4 of a fake amount of "extra income" that would be sufficient for your withholding to be okay. (I'm not aware that it would both suggest extra income in Step 4(a) and "extra withholding" in Step 4(c) but those two things both increase withholding.) One consequence of this is that if you or your spouse's current W-4 setting has Step 2(c) checked, the amount you can expect to be withheld if you send in a new W-4 will NOT simply be your old withholding amount plus the Step 4 new amount; it'll also be adjusted downward because switching from Step 2(c) checked to Step 2(c) unchecked takes out less withholding by default. This makes anticipating how your paycheck withholding will change when you hand in the new W-4 a bit challenging if you're not familiar with Step 2(c)'s effect. There is a publication called Publication 15-T you can get as a pdf from IRS.gov if you want to see tables showing roughly how much is withheld based on paycheck size, paycheck frequency, filing status, and whether you have step 2(c) checked or not. Perhaps consult that and use it to help anticipate what your withholding would be and compare it to what your tax will be (Form 1040-ES booklet has formulas for estimating that). If you're far off you could then determine what amount of "extra withholding" you want in Step 4(c) which is a per paycheck amount. That would be a way to figure the adjustment "by hand." Lastly -- you asked about how to enter your income information into the online tool. They want gross income in the first place, but later screens ask you about things like insurance or HSA amounts that should be deducted from that because not taxable. Whether you give them the lower amounts and then disregard the fields about insurnace and HSA, or you give the gross amounts first and then carefully enter the amounts to be disregarded, you should be able to confirm that it has a good idea of your taxable income over the full year, because some screens will have you confirm that and the final screen will talk about your overall income subject to tax. I can see how confusion about what to enter for income could certainly cause incorrect results from the online tool. It's not a really super user friendly interface. More on reddit.com

Without knowing all your inputs it's hard to explain why or what happened. More on reddit.com