I'll provide an explanation of why the GST suspense transaction shows two entries with the same payment that appeared.
It might be the payment transaction was added instead of matching them. If it's the case, the amount will be duplicated. To sort this issue, I suggest matching the transactions rather than adding them. Match means QuickBooks matched the downloaded transaction with the one you already entered. This links the two so there aren't any duplicates. All you have to do is make sure the match is correct.
Before matching them, I recommend undoing the transaction that already added.
Here's how to undo:
From the Banking tab, select Banking.
Go to the Reviewed tab.
Select the transaction.
Click the Batch actions drop-down, and then select Undo.