I too am having the problem with >2% s-corp shareholder including HSA in Box 1 and NOT Box 3 and Box 5. It seems like it should be easy for Intuit to do this because the same treatment is being done for S-Corp Medical Insurance (subject to FIT-Box 1, but NOT subject to Medicare/SS (Box 3 and 5). They just need to create the same pay type as S-corp Medical Insurance but call it something like HSA >2%. Should be SUPER EASY. I am using Quickbooks Payroll Enhanced in conjunction with Quickbooks Desktop Pro so hopefully they will be able to port the solution to this into that program as well.
