Hey there, @computerwild.

Thanks for following the troubleshooting steps recommended above.

I've also replicated the steps and the sample custom field that wasn't set up as Public aren't showing in the email. Please see the screenshot below as your reference:

Since you're still getting the same issue. I'd recommend reaching out to our QuickBooks Online phone support. They have the available tools that can perform screen sharing session with your account in a secure environment. This way, they trace where might this issue is coming from. 

Here's how you can reach out to them:

1. Click the Help icon.
2. Hit the Contact Us button at the bottom. 
3. Enter your concern in the description, then click Let's talk or Continue.
4. Select Get a callback.

You can also check out the How to add custom fields to invoices page to learn more about adding important information on your sales forms.

Don't hesitate to tag my name in the comment section below if you have other concerns or questions. I'm always ready to help. Have a good one.