Hello,
As you can see, I have a taxonomy Product Category connected to Product Item.
Since some time I cannot find the menu point under Products for editing/creating Categories and I cannot select a category for each product (a tree with check boxes was appearing on the right before Featured image).
The last screen shot with Product Categories is what I displayed by typing the url and shows the missing categories.
If you need, I can give you access to the admin panel.
Thank you for your concern.
Sergey Karov