On the screen with the HSA breakdown, the deduction is $0 and tax-free employer contributions is $XXXX. Does my payroll contribution roll into the employer contribution or is that separate?
The hsa contribution has already been made pre-taxed as evidenced by the code w on the W-2 form. You do not get to deduct it from your taxes again. The program is handling this correctly.
your payroll deduction rolls into the employer contribution
is it confusing... what is on your W-2 (box 12 code W) is what the IRS and TT call 'employer contribution', even though, it is money you earned that is put into the HSA.
there is another question elsewhere in TT where it asks how much did YOU contribute to the HSA. This trips a lot of people up! They are asking whether you sent money directly to the HSA outside of you paycheck! that is considered 'employee contributions'. If you duplicate what is on the W-2, it will double the contribution and many get the warning that you over contributed for the year!