I recently upgrade to WP 3.0 and AT 3.5.3 . I am now using the new menu options included with WP 3.0 and now integrated into AT. Everything is great - except for some reason using the %page-right or the %cat-right expressions in the "Style and edit header area"-> "Configure Header Area" option box will align the menus to the left. %page-center and %cat-center work correctly as does %pages and %cats.
Our website: www.habitatmagicvalley.org
The Configure Header Area options are: %logo %page-center %image %cat-right
As you can see the %cat-right menu is actually on the left!