i also had this problem. the problem is that you are adding action to *admin_init* … try something like this:
add_action( 'admin_menu', 'remove_unused_menus' );
function remove_unused_menus() {
remove_menu_page('link-manager.php');
remove_menu_page('edit-comments.php');
}
notice the use of *admin_menu* instead of *admin_init*
some require admin_init…but i forget which/why.