Okay, we fixed it.

This is one site in a multi-site

We had network activated WooCommerce.
Although the WooCommerce tab showed up in the customization menu the “Enable WooCommerce On Menu” option in header options was missing.

So… we network de-activated WooCommerce

Then activated WooCommerce on just the one site we were having the issue with.

The “Enable WooCommerce On Menu” re-appeared! And works.

We were then able to network activate WooCommerce again and the option remained working.

Thanks
Chris + Jon