Did you make an entry for Qualified unreimbursed medical expenses paid 2 lines below the entry for the distribution? That just zeroes out the distribution and there would be no income.  Review the 8889 Part II to see the two entries.  

"Qualified unreimbursed medical expenses paid using HSA distributions (and not entered elsewhere)

Enter the total of qualified unreimbursed medical expenses paid using HSA distributions (and not entered elsewhere).

The program uses this amount to reduce the taxable amount of HSA distributions in the HSA Distributions section of Form 8889."