When you re-enter the HSA interview (Deductions & Credits->Medical->1099-SA, HSA, MSA) or something similar, it varies from product to product), you will see a screen headed "Let's enter [name]'s HSA contributions".
The first line is the code W amount from box 12 of your W_2.
The second line is the amount of HSA contributions that you sent directly to your HSA, NOT through your employer. Therefore, do not put your payroll deductions on the second line, even if you think that they are "personal" contributions.
Let us know what happens.
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