I use custom taxonomies rather than categories to arrange my posts, due to the nature of my blog, and create these using the Custom Post Type UI plugin. This had been working very well, and I was able to create custom menu widgets for navigation. However, when I last visited the custom menu creation page in WordPress, none of these were visible, and so I was unable to update my menus. I tried deleting all my taxonomies and starting again, but only one of the new taxonomies appeared, when there should have been four.
I cannot understand why this is happenning. My only thought is that I recently renamed my 'wp_' table prefix. I was wondering if I might need to make changes because of this. Please let me know if you have any other ideas. Many thanks!