Your HSA contributions and distributions are made tax-free only when form 8889 is complete. This form is completed only when you finish the HSA interview (Federal->Deductions & Credits->Medical->HSA, MSA Contributions).

You need to go all the way to the end of the HSA interview (until you are returned to "Your Tax Breaks") because there are questions all the way to the end of the interview that affect your HSA tax status.

TurboTax has to do some calculations out of sync with what you are entering on the screen; that is why it's not a good idea to watch the refund meter too closely while you are entering information into your tax return.