Same situation for me. It did as Helena C mentioned above... went down, then went up to the original refund amount. But once I answered that I had a high deductible health plan (HDHP), it went up significantly.
Another response to a similar question that I found said that turbo tax incorrectly thinks you owe the tax if your w-2 shows a W in box 12, thinking you don't qualify for tax-free treatment on these contributions to your HSA. It's only after you confirm that you have a HDHP when entering your 1099-SA info that turbo tax realizes you DO qualify for tax-free treatment.
