Hi Jodie,
When the annual leave was recorded in the pay runs and the pay runs were finalised, this would have posted journal entries in QuickBooks and the PAYG figure in the prepare BAS section would be reflected from them.
I would first check the PAYG Withholding Report, which can be found in Reports in the Employees tab, to ensure that the PAYG was captured correctly in the pay runs. If that was recorded incorrectly, unlock the affected pay runs and adjust the PAYG before finalising them again.
Next, check the PAYG Withholdings Payable account in the Chart of Accounts (Select the Gear Icon on the top-right corner of QuickBooks, then select Chart of Accounts). Each journal entry in this account represents one pay run. Ensure there are no duplicates or missing journal entries. If there are duplicates, delete them. If there are missing journal entries, locate the pay run and unlock, then finalise it again so the journal entry gets posted again.
As long as the amount in the PAYG Withholdings Payable account is correct, then it should reflect that figure in the BAS section.
Hope this helps!
Bonny
