Thanks for reaching out. You'll want your settings in Square to match that of QuickBooks. e.g. The tax codes selected need to match exactly.
Please see here for more information on Sync with Square and GST.
We also have a general overview of the app and settings here.
Please let me know if you have any other questions at all.
The settings all appear to be correct. The mismatch may be with how the GST codes are showing on the Square Invoices. If these don't match QBO exactly the amounts won't be allocated to the correct accounts.
I would suggest reaching out to Square to see if they're able to identify anything on their end otherwise please contact our Support Team so we can do some more detailed troubleshooting.