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Hi cdwilliams2785,
Did you assigned a GST code on each line of the Journal Entry? If so, try to edit the journal and assign GST code on Line 1 only. Furthermore, since you set the journal entry to Inclusive of tax and the accounts affected is a GST Liability this will still show the total amount of the transaction in the bank reconciliation.
We'd recommend viewing the Transaction journal of the journal entry for you to check the accounts affected. Here's how:
You can check these articles about how to create a journal entry and perform bank reconciliation in QuickBooks Online.
Please know that you're always welcome to post if you have other concerns.
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