I have a multisite setup using Custompress to create 3 custom post types, 1 custom taxonomy and a handful of custom fields. I have also added some posts under each post type and created some terms in the taxonomy.
The issue I am having occurs when using New Blog Templates and it is related to the custom taxonomy, which is called "Channels". I can create a new site and choose the NBT from the dropdown. The new site is created and looks identical on the backend. All settings, custom setups and content are present. But the wp_list_categories() function in the theme comes back empty.
For the initial site, I have wp_list_categories() displaying a linked list of all terms defined in the "Channel" taxonomy, plus I link to it from each post.
In the created site, when I click on an individual post, it does display what "Channel" that post is in, but the link to the archive for each "Channel" comes back 404. It seems there is somewhere that wp_list_categories() looks to find this listing and that is not being copied by NBT.