GST Summary reporting difference in Box1,2,3 vs total revenue. Unable to view content for Box 2 and 3 to determine why the difference

Hello there, usertzetian-yeo.

I've got the steps so you have accurate GST Summary reporting in QuickBooks Online. This way, you can ensure your tax data stays accurate for filing.

Yes, you're correct that one of the factors of the discrepancy in the GST Summary reporting is the inaccurate configuration of the taxes in the application. To fix this, I recommend reviewing and making sure that the GST settings for your product items and customers are correct.

Here's how for items:

1. Select the Sales menu at the left panel and Products & services.
2. Find the particular item you want to assign a tax category to, then select Edit.
3. Go to the GST dropdown menu, then find and choose the specific GST that fits your item.
4. Complete your item’s info.
5. Save your item.

Once done, ensure that you have your customers' correct tax status, billing address, and shipping address entered in QuickBooks Online. Here's how to double-check and edit your customers' info in QuickBooks.

Additionally, you can also open per transaction that is causing the difference in the GST Summary reporting. This is done to review the tax rate associated with each entry and make changes if needed. 

However, if you made a manual adjustment for GST amounts, you need to review them to verify you are not contributing to the discrepancy.

Lastly, you can read this article if you need steps on how you can add group tax in QuickBooks: How do I set up sales GST rates and use them on forms? (International QBO).

I'm always here in the Community to help if you still have other concerns or follow-up questions regarding GST Summary reporting, usertzetian-yeo. I'll be glad to help. Take care.