Custom Post Type Categories

Hi I’m using your plugin to display an index for a Yada Wiki category I’ve created. It works great except I cannot choose the category for the custom post type, it only displays categories for the normal posts and none that are created for the Yada Wiki plugin.

It’s not a huge problem since I’m only using one category for now, but in the future it might be useful if I create different categories for the custom post type that I want to display somewhere else with your plugin.
Thanks ??