Fixes the problems (post WordPress 3.1) with Custom Post Type Menu classes not being added correctly.

wp-custom-post-type-class-fix.php

<?php function remove_parent_classes($class)
{
  // check for current page classes, return false if they exist.
	return ($class == 'current_page_item' || $class == 'current_page_parent' || $class == 'current_page_ancestor'  || $class == 'current-menu-item') ? FALSE : TRUE;
}

function add_class_to_wp_nav_menu($classes)
{
     switch (get_post_type())
     {
     	case 'projects':
     		// we're viewing a custom post type, so remove the 'current_page_xxx and current-menu-item' from all menu items.
     		$classes = array_filter($classes, "remove_parent_classes");

     		// add the current page class to a specific menu item (replace ###).
     		if (in_array('menu-item-35', $classes))
     		{
     		   $classes[] = 'current_page_parent';
         }
     		break;
     }
	return $classes;
}
add_filter('nav_menu_css_class', 'add_class_to_wp_nav_menu');