Categories, Tags and Sorting Not Working

In an effort to help you, I started a new ticket on this since the other thread seems abandoned by WPMUDEV.

It doesn't work at all. If you go to the products STORE page of the site, it shows the category counts which is correct in the drop down and on the back-end they are correct, but it displays on the front end one product, incorrectly. It sorts everything incorrectly.