The ‘duplicate’ submenu vanishes, but (at least in my case) after selecting MyMenu, there was no page contents.
So as to display sth, I’ve used this:
add_menu_page('MyMenu', 'MyMenu', 7, __FILE__, 'print_submenu_1');
add_submenu_page(__FILE__, 'Submenu 1', 'Submenu 1', 7, __FILE__, 'print_submenu_1');
add_submenu_page(__FILE__, 'Submenu 2', 'Submenu 2', 7, 'submenu2', 'print_submenu_2');
As for Thickbox, look in nextgen/thickbox/thickbox-pack.js