remove_menu_page not working on some menu items

I have a custom plugin that I’m using to hide admin menu pages from Administrators so that they can only be seen by Super Admins. It was working until I upgraded to 3.8.1, and now some admin menu pages that are supposed to be hidden are showing.

Here’s the function:

function s_remove_menu_pages() {
     if (!current_user_can('manage_network')){
	remove_menu_page('index.php');
	remove_menu_page('users.php');
	remove_menu_page('tools.php');
	remove_menu_page('options-general.php');
     }
}
add_action('admin_init', 's_remove_menu_pages', 999);

All of these pages except users.php are showing in the menu for Administrators.

I’ve tried using admin_menu instead of admin_init. I’ve tried changing the number from 999 to a different (smaller) number.