No, the issue is probably this:
When your employer creates your W-2, your employer removes your code W amount from Wages in boxes 1, 3, and 5 on the W-2. This is why no deduction appears on your return, because the code W amount (your employer's and your contributions through payroll deduction) were never in your reported income in the first place.
It sounds as if your employer correctly removed the HSA contributions from your Wages but forgot to enter the code W amount in box 12 on the W-2. In this case, then you got the corrected W-2 with the code W amount, then you would not (in most cases) notice a difference on your federal return, because the deductions (actually, an exclusion) was there but the code W was not.
So why is the code W necessary? Because it is used to help TurboTax calculate whether or not you made excess contributions to your HSA. In addition, two states (CA and NJ) do not permit HSA deductions, so the code W amount has to be added back to state income.
So if your employer had removed the HSA contributions from Wages both times, your HSA calculations are fine.
