You need to get a corrected W-2. HSA is properly recorded in Box 12 with Code W. You have a bigger problem than the program not picking it up. The IRS, when they get their copy of your W-2, won't be able to reconcile Box 14 Sec 125 with your Box 12 HSA.
Box 12 codes:
- W — Employer contributions (including amounts the employee elected to contribute using a Section 125 cafeteria plan) to your health savings account (HSA).
