QB Issue Resolution:

First you will need to Delete the incorrect payment made as an Instalment. To do that, search for the amount of the payment in the top middle search function. Make sure you have Unmatched this Transaction from Online Banking first otherwise it won’t let you Delete.

Afterward to make the correct regular Payment, make sure you are recording by going to Sales Tax – View History, then selecting the Record link in the chart, under the Payment column next to that appropriate filing.

Resolution for Issue 'My GST Payments are not showing up correctly.' available: Yes (Solved).
Source: Intuit Community forum.

My GST Payments are not showing up correctly.: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

Support for GST
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Error Recovery for GST [Canada]
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