The amount with code "W" in box 12 on your W-2 is the sum of your employer's contributions to your HSA and your payroll deductions for your HSA.
Normally, this amount is not taxable, but that is only when form 8889 is properly completed.
Form 8889 is not completed until you finish the HSA interview (see the screenshot below) at Federal Taxes->Deductions & Credits->Medical.
Be sure to go all the way to the end of the interview (until you return to "Your Tax Breaks").
For this reason, your code W amount appears to be taxable (reducing your refund) until the HSA interview is completed. Go ahead and complete the interview.