Mike,
I am using the Custom Post Type UI plugin. I also just added the GD Custom Posts and Taxonomies Tools. The other plugin I am using is just one I created myself to create a custom post type of “Movies” with several different taxonomies. (This was for testing all the changes being developed for WordPress 3.0.)
The results were that none of the taxes from my plugin worked with your plugin, although they work for everything else.
The taxes created with the Custom Post Type UI plugin worked, even though it has not been updated to work with the WP 3.0 changes.
The Custom Posts and Taxonomies Tools plugin has been updated to work with WordPress 3.0 and the taxes I created with it do not work with your plugin either.
I haven’t had a chance to explore your code but I wonder if the problem might be with “is_taxonomy”. It would seem that the plugin is recognizing some taxes but not others. And why would it ignore taxes updated to work with WP 3.0 and work with ones not updated?
To answer your question, yes, I made sure there were terms in the taxonomies I checked.
You mentioned that all post types and taxonomies were created in functions.php. All the ones I am mentioned were created with plugins.
The one which works the best is the “movies” plugin I created, but that’s because I kept changing it to be compliant with every nightly build.
If “is_taxonomy” is failing somewhere along the line, that is a serious bug and worth checking out.
Ron