Double release today for GD Taxonomies Tools, both Pro and Lite version. Both versions contain several minor fixes, but more importantly they are compatible with latest development build of WordPress 3.0 and changes core developers made to custom taxonomies handling.
Finally, WordPress 3.0 supports hierarchical custom taxonomies, and plugin will now allow you to make such taxonomies and use it. Also, some elements in the custom taxonomies structure have changed and for now plugin handles both old and new formats well. If more changes are introduced in WP 3.0, plugin will follow soon after.