The problem is Box 1, 3 and 5, even box 18 has not been reduced by the EMPLOYEE contributions that are in Box 12- W. This is a huge issue that may be the reason people are getting no refunds and having to pay Federal and State taxes they should not be. HSA taxes should be also excluded from Soc. Sec. and Medicare taxes and almost all states it is also exempt from.
This is a major problem I just discovered and are taking in to my HR department.
