Ok I've just found the Audit report

It appears that the PAYG tax rates change depending on how much I pay myself on any given month.

On one pay run, I have a PAYG rate of 20.46% on another 28.6%

Does QB assume that if I select the pay run is for approx 1 month it will assume a total payment for the year to be 12 times the amount and tax accordingly?

Generally, I select monthly when doing a pay run even though the income or funds available to pay myself may be for 2 or 3 months.

or to put it another way, If I pay myself $10000 for a pay run which I have selected for a month does it then work out the tax as if I were earning $120,000 per year when in reality I am earning only $45,000