Thanks for the information and screenshots.
We suppose that the the plugin or theme that ensures products and portfolio custom post types for you removes all 3rd party metabox from these admin pages. In this case our plugin create the manual relationship metabox, but it is removed. (It is only a assumption.)
What plugin or theme do you use that creates product and portfolio post types?
If this available for us, we can see whether it removes these metaboxes or not.