I use this plugin when developing my plugin (Cleverness To-Do List). My plugin creates it's own menu item and subpages in the WordPress admin.
Before I upgraded to version 3.4 of WordPress, the debug bar worked as I expected, showing the correct number of queries for the pages. Now it only shows that there are 14 queries on each page (and it doesn't list any of my plugin's queries).
I use add_menu_page and add_submenu_page to add the menu items.