You are not doing anything wrong - it's just that TurboTax is set up to handle the normal use of code W in box 12 on a W-2 and not the special case of a 2%+ owner of an S corporation.
In the case of a "normal" employee, the HSA contribution paid by the employer and the employee (by payroll deduction) is removed from Wages in boxes 1, 3, and 5 on the W-2. But in the case of a 2% owner of an S corp, the HSA contributions are not removed from Wages in box 1 on the W-2 but are included in these Wages (i.e., after-tax).
Note that the same HSA contributions can still be removed from Wages in boxes 3 and 5 on the W-2 because they are not subject to either Social Security or Medicare taxes (FICA). This is described in IRS Notice 2005-8 (https://www.irs.gov/pub/irs-drop/n-05-08.pdf).
So, your HSA dollars coming from the S Corp are after-tax (as you noted). You recover your tax benefit by making a direct (“personal”) contribution to your HSA. Normally, this would appear on line 25 on page 1 of the 1040 as an adjustment to gross income. Thus, you have ultimately received the same benefit that any employee would concerning the HSA contributions, you just have to make the entry manually to make the amount appear on line 25.
You will enter the HSA contributions on the “Let’s enter your HSA contributions” screen in the HSA interview (Federal->Deductions & Credits->Medical->HSA MSA Contributions) – see below. You will enter your contribution on the second line (where the $2,000 is), because that’s where after-tax contributions go.
As noted, this will appear on line 25 on page 1 of the 1040 as an adjustment to gross income.
Note: if you are filing an Alabama, California, or New Jersey state return on your your personal return, come back and comment on that - these states use the code W in box 12 to add back the HSA contribution (HSA contributions are not deductible in these states), and I am not sure if TurboTax will handle the situation correctly unless we tell it to ignore line 25 in these states. For the other 47 states, however, you will be fine.
