The problem seems to be this line towards the bottom of header.php:
<?php slider_menuparse(wp_list_pages('sort_column=ID&depth=1&number=7&title_li=&echo=0')); ?>
By specifying number=7, only the first 7 pages will be looked at, even if they are not all top-level pages (depth=1). Remove the &number=7 text, and ALL top-level pages will be shown. Provided you have exactly 7 top-level pages, then the behavior will be as you wish.
Note also that changing ID to menu_order will sort the pages in menu order, using the Order attribute of the page.
