The IRS assumes that HSA contributions are income until you prove that you had qualifying HDHP coverage. The IRS also assumes that your HSA distributions are taxable until you prove that they were for qualified medical expenses.
Thus when you enter your W-2 with the code W (HSA contributions), the code W amount is added to income until you go through the HSA interview and complete it. When you tell TurboTax that you had HDHP coverage, the income will be removed. Ditto with the HSA distributions.
Just make sure that you go through the HSA interview to the end, and stop watching the Refund Meter so closely. You'll be OK.
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