Our system makes use of an Average Tax Calculation which means that the Year To Date taxable remuneration is used to calculate the tax and not the current monthly figures. So when taxable remuneration is fluctuating from pay period to pay period it will result in a credit amount to balance to what the year to date tax amount should be on the year to date totals processed. A final Tax calculation is done either in February (as this is the final period of the tax year) or when the employee is terminated (that's why you need to terminate the employee before paying the final payslip). 
To view a detailed tax calculation for a specific employee select "view tax calculation" on the employee payslip tab.
help.accounting.sageone.co.za/.../za-pay-tax-calculation-view.html