When you access t-code PC_PAYRESULT for one of these employees you can check when a pay was executed. Was it first executed (and going retroactively) before you made the changes to the PAA Control Record and to the employee's IT0003 ?
If Payroll is not yet terminated, did you try to delete the employee's Payroll Results for the current pay, check the IT0003 and re-execute Payroll for that employee?