I finally figured this one out! 

I had not inputted the actual taxable amount into QBO (PAYG + amount owed to the ATO)

I use an "Income Tax Payable" account to record the actual tax owing to the ATO, then I used journal entries dated at EOFY which split the amounts that I paid to the ATO and the remaining PAYG amount. I could then match those amounts using journal entries to zero out my PAYG Instalment liabilities account. 

My mistake was only recording the debt owed to the ATO, therefore I wasn't recording what I actually had paid the ATO in advance through PAYG. 

I hope this helps someone who has the same problem as I had.