I think the 5498-SA is being filled out correctly and my employer is telling the HSA custodian that the first contribution of the year is actually for the previous year. Box 3 does seem to have this amount. The hard part was just understanding what was going on. Rather than the IRS keeping things simple and just letting box 2 contain the contributions that are attributed to the current tax year (regardless of the year actually deposited), it forces box 2 to include all contributions (deposits) made during the calendar year, and then adjustments have to be made with box 3, which means also you need the previous year's box 3 to actually calculate contributions attributable to the current tax year.
(this year's box 2 + this year's box 3 - last year's box 3) = W2 line 12 HSA amount
I'm not sure why this type of accounting is needed.
