OK, we have a problem. If the distribution is considered taxable, it will be on line 21.
Please Search (upper right) for "hdhp" (lower case, no quotes), then jump to hdhp. The next screen should be HSA Summary. What is the amount for taxable distributions? Is it zero?
Now click "Edit" on the summary screen to restart the HSA interview. Enter the 1099-SA by clicking on "Edit" next to your 1099-SA. Continue through the three screens for the 1099-SA until you come to the screen that asks "yes/no were all the expenses used for medical expenses?". Is it marked as "yes" or "no"? If it is yes and you have no entry on line 21, then all I can advise is to delete all your HSA information and start it over.
To delete your HSA information, please do the following:
The safest - although brute force - way to fix this is to do the following in this order:
1. make a copy of your W-2(s) (if you don't have the paper copies)
2. delete your W-2(s) (use the garbage can icon next to the W-2(s) on the Income screen
*** Desktop***
3. go to View (at the top), choose Forms, and select the desired form. Note the Delete Form button at the bottom of the screen.
*** Online ***
3. go to Tax Tools (on the left), and navigate to Tools->Delete a form
4. delete form(s) 1099-SA (if one), 8889-T, and 8889-S (if one)
5. go back and re-add your W-2(s), preferably adding them manually
6. go back and redo the entire HSA interview.