issue with categories after update

If I look at my posts in the dashboard, they all contain the appropriate categories, but if I look under ‘categories’ all but the main one are empty.

if I call on ‘hp wp_list_cats’ it only lists the one main category.

If I link directly to the page (i.e. wordpress/category/category_name/) it works fine.

BLOG is here:

http://www.halfbakedschemes.com

Any help?

TIA.