Our HSA Deduction is set up to be pretax in the setup area (before Federal and SS). When we run our 941 Preparation Report, however, the amounts are not being reduced for HSA contributions (it is reducing by Health Insurance deductions but not HSA - both are set up the same).  When I run some quick checks, it also looks like during the payroll calculation, HSA amounts are not reducing taxes. Is there another setting that would impact the pretax status of this deduction? 

Is there a report that shows what is used in the calculations? It is set up correctly in the deductions area, but I'm not convinced it's being calculated correctly.