Contact your HSA custodian (or look at your statements online) and ask for the amount of contributions to your HSA - actual cash contributions, not things that your employer calls HSA contributions.
The amount of actual cash contributions to your HSA is what should be reported in box 12 with a code of W on your W-2.
You do not need the 5498-SA to file. You should be able to cross check the HSA transactions in your account with the code W amount. If they match, your W-2 is fine.
I suspect that there is a terminology issue in that your employer is calling things an HSA program or contribution when it's actually not. You sound like you have it in hand.
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