This may be a matter of timing. If you say that you have HSA contributions through your employer, then the contributions are considered taxable until you demonstrate adequate HDHP coverage. Since HSA contributions through your employer are removed from Wages before your W-2 is printed, the contributions have to be added back to income (making your taxes go up temporarily) until you go through the HSA interview.
I see that you said that your refund goes down when you say that you have HDHP coverage. This, of course, is not right. We encourage taxpayers not to watch the Refund Meter too closely because there are things happening in the background that are out-of-sync with your return.
Since you believe that you have entered everything correctly, tell us step by step (in excruciating detail) what you entered vis-à-vis your HSA, and when the Refund Meter changed either up or down.
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