I've a slight problem with one of my website, which use a particular structure of custom post types and custom taxonomies.
Indeed, my custom post type must NOT appear in the website, I only use custom taxonomy to show entries for each term (my site is a custom directory...)
When I include (uncheck) my custom taxonomy, it doesn't appear in sitemap files :-(
I tried to uncheck the custom post type, but my custom taxonomy doesn't appear also. Articles doesn't appear in the sitemap also because I've checked (I don't use them) : I don't know if there's a relation or not.
Notes that on another website using 3.0.4 WordPress version, it works well !