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Hi user61405,
Do you have the same product or item wherein GST code is not recognised? Let's check a few settings in QuickBooks Online.
Also, you may try to check the default tax setup (if it is set as inclusive or exclusive of tax) in QuickBooks Online to see if it matches with Connect to Square app. Here's how:
In any case, there were still no changes after modifying your app settings, you may contact our support team to further check on your account.
You can also check this article for your reference: Connect your Square account to QuickBooks Online.
Feel free to drop a comment below if you have any other questions.