Hi maddoglee,
By design once a BAS lodgement and payments or refunds are made it will all clear through the ATO Clearing account, and the Liability accounts will track the changes made to each category. Then, once it's year-end financial when you lodge your tax returns and enter any applicable journals those accounts will be cleared.
I'd recommend checking the settings in your GST to verify if PAYG Instalment is correctly set up. Here's how:
- Click on the GST Center.
- Click on the Settings button, and select Tax settings.
- Check if Company Income Tax (PAYG Instalments) is set up correctly like lodging frequency and accounting method.
If you've checked the above and the settings are correct, I'd recommend contacting directly our Customer Care Team to help check your PAYG Instalment Liability account. That way one of our support can check the account in a secure form.
As always feel free to reply on this thread if you have more questions. We'll be sure to get back as soon as we can. Enjoy the rest of the day!
