Pay Class Not Working

We have set up a pay class tied to a specific pay code and added a handful of employee deductions to the pay class.  When we process payroll, creating multiple checks based on unique pay codes and check groups, the employee deductions are withheld against the one associated pay code which is what we wanted.  But the kicker is when you add in company paid deductions into the mix, it is deducted against not only the pay code in the pay class, but is deducted with every check created in the payroll regardless of the pay code.  Any ideas why when set up as employee deductions that work, company deductions associated with the same pay class ignore the pay class assoication?