Hi Sam,
I am having the same issue. I found a work around for this.
Your settings may be a little different to mine but here is what I did:
Note: This will only work if you have user approval to post journals. The Tax Code we have for PAYG Withholding is called BAS-W2 on our file.
1. The IAS journals posted by the GST Module for the months of January and February had no BAS-W2 tax code for the PAYG Withholding line item. I wasn't able to modify these journals to include a tax code so instead I copied these (i.e. made a duplicate journal on the same date as each of them).
2. In the duplicate version I included the BAS-W2 tax code on the PAYG Withholding line (Dr).
3. Then changed the Cr line to the same PAYG Withholding account but left the tax code blank.
4. I was then able to run the BAS and get the correct PAYG for March.
Hopefully this won't have any implications for June BAS.
It would be great if Quickbooks could include the tax code in the automated journal that is posted when you process the IAS lodgements through the GST module. It seems to be a backend configuration as I can't find a way to change this myself.
I hope this work around helps you.
