Review your Payroll Withholdings account settings for the employee and the employer Withheld accounts with the employer accounts set for the Payruns ( Payruns > Settings) and the employee total to accounts for CPP EI and TAX (or FICA MEDI FIT and SIT if USA Payroll).

I suggest that when you issue Tools > Pay Withholdings that you save the settings for each separated payroll by clicking the new button and save the Current Settings name to a unique separated payroll name.

Regards to All,