Welcome to the Intuit Community, BOS49.
Thanks for being part of the QuickBooks family. I want to ensure the data showing on your VAT Detail Report are correct.
We’ll have to check how transactions are recorded and the tax codes are used in QuickBooks. However, the process requires accessing of company file which can only be performed by our Technical Support Team.
For this reason, I recommend you get in touch with them. Our specialists can check the data in a secure environment.
If necessary, they will perform a screen-sharing session with you to determine why there are two HMRC agencies, and why the VAT return boxes and EC transactions are not found on the report.
In your browser, enter this link: https://help.quickbooks.intuit.com/en_GB/contact.
In the What can we help you with? section, select the issue/topic.
On the Here's how to connect with a QuickBooks expert about page, click on the Get Phone Number button to see the support number. Note: Open: 8AM-8PM (GMT) Mon-Fri.
After contacting them, your VAT return boxes and EC transactions should now appear on the report.
For future reference, I'm also adding an article with detailed information on how to file the tax return via MTD: QuickBooks Desktop VAT e-filing & Making Tax Digital.
Keep me posted about how things go after contacting support. I want to make sure this is taken care of for you.
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