Hope you don't mind me jumping in here, but I think I have this same issue or, more appropriately, same question.
I'm using your plugin to create a CPT called Bulbs. We're going to offer replacement light bulbs of various types. There are several of each type. Normally this would lead me to believe that I would create 'categories' representing the types and add a new 'bulb' and assign it to the proper 'category'. Which is what i've attempted to do. So, I have the following:
CPT named Bulbs
Need for categories such as
And, the ability to add 'bulbs' that would display within those categories. In the CPT setup I chose the checkbox next to Categories which then displayed Categories in the Bulbs menu section. I then added my list of Categories only to find out those also extend to the regular Posts categories as well (in other words, the categories I created show in both the Bulbs / Categories and Posts / Categories areas. I thought they would be specific to just Bulbs).
The goal is to have the bulb categories displayed in the main site menu (A Lamps | PAR Lamps | etc. | etc.)
However, what's happening is when adding those categories to the menu and clicking on them, no results display. This is where i'm totally confused, how to connect the CPT to a categorical display.
I've created a special post template that displays various custom fields. That part is taken care of. The part that is whacking me out is the association to a category to get a product list display.
Any help here would be greatly appreciated!