Could you elaborate further Steve. Which programme are you using? What is the frequency of your pays? What is the tax status of your employee - TFT, etc Are there any variations to the way tax is to be withheld - HELP? flat tax; additional tax?
The PAYG tax calculations have been created to comply with legal requirements for withholding tax (and approved by the ATO) so there would only be very exceptional circumstances whereby you need to adjust the amount calculated.