preprocess_menu hook not being called for these menus

I am finding that the hook_preprocess_menu() is not called when using this module to show a menu. I see you have your own manipulator hooks, but why is this module not just relying on the built in preprocess_menu hook? It seems that since this is displaying a drupal 'menu' that it would be running the preprocess_menu() on those. I actually feel like drupal should be doing that and so maybe it is just a problem with the way the menu tree is being retrieved. Thanks for the help.