When you review the GST module in QBO, it only shows you the amount currently owing based on your payment time frame.
For example, if you're set to pay Quarterly (as many businesses are) it will only show you the amount of GST accrued in the current period; whereas, the balance sheet includes all amounts for all periods historical.
To start, you'll want to review the company's records on the CRA site and see if they also show the company in arrears, or if it shows historical payments made. It's possible the payments were actually completed and just never recorded in QBO.
Hope this helps!
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