Hello, 

I am having this same problem, but your answer refers to "GST liabilities". The question is about PAYG Instalment liabilities.

I cannot for the life of me, figure out why Quickbooks does not record my payment of the PAYG Instalment when I pay the BAS. 

I thought it would work the same as the GST liabilities account. 

My PAYG Instalment liabilities account is forever going negative even though I've been paying the instalment (through the BAS)