@andrewF
"However, when this number is entered into line 9, it indicates that the full $7,000 in that box that was added to my HSA is comprised of employer contributions, when actually it was $1,500 from my employer and $5,500 from me."
The code W amount should be on line 9, because the "employer contribution" is the sum of what your employer contributed PLUS what you contributed by means of payroll deduction. It's counter-intuitive, but that's the way the IRS uses the terminology.
As noted elsewhere, your $5,500 payroll deduction was removed from Wages in boxes 1, 3, and 5 before your W-2 was even printed, so of course you don't see a deduction for the $5,500, because it was never in your income in the first place.
"To confuse things further, my 2017 and 2018 W-2s only list the $1,500 employer contribution. If the comments here are correct that Box 12 code W should include both employer and employee contributions, then the 2019 W-2 is correct, but being misinterpreted by TurboTax, while the 2017-2018 W-2s were incorrect but resulting in the correct answer."
If you had payroll contributions in 2017 and 2018 which were not reported with the code W amount on your W-2, then, yes, your W-2s in those years were wrong.
The way to fix this would be to amend your 2017 and 2018 returns and look for the screen in the HSA interview that asks if your employer reported any other contributions to your HSA. Answer "yes" then place the amount of your payroll deduction on the line "HSA contributions not reported on your W-2".
