hi Freman Cazza1 gevans
For your information I brought a similar problem with PAYGW calculations to the attention of the ATO and the Tax Board years ago.
It related to the calculations for people who had two jobs and the without tax free threshold was not working correctly. Try their on line calculators even and the same problem happens there.
For example an employee who say earns $1,200 a week from one employer would be taxed $231 and be all good (hopefully at year end). But if that employee works at one employer and gets $800, claims threshold Tax is $101, then they earn $400 and dont claim threshold their tax is $90. They have now paid $191 between the two jobs.
If this employee does this on a regular basis at the end of the year they will be underpaid $2,080.00
The ATO's response was, Well the employee can make a payment plan!