Wage Basis Rules not behaving as expected

We recently set up wage basis rules for some of our taxable benefits in PA Locals. The Primary Classification that we touched was Imputed Earnings, secondary classification was Personal Use of Company Car. The update worked to make the deductions taxable, however when we did this it impacted some of the other classifications ( one of the secondary classifications was custom, but not all of them). We've confirmed that Pretax, Deferred Compensation 401k was impacted as well as a custom secondary classification under Supplemental Earnings. Our Regular Salary element was not impacted though, and that has a primary classification of