Box 1 of Form 5498-SA is only for reporting contributions to an Archer MSA, not for reporting HSA contributions. If the account is an HSA, the custodian must not make any entry in box 1.
It's hard to believe that an HSA custodian would make such a reporting mistake. Are your sure the amount of your contribution made for 2016 in 2017 isn't in box 2 of the 2017 Form 5498-SA (where it should be in addition to appearing in box 3 of the 2016 Form 5498-SA).
