I've noticed that I have to move the sub-pages around in the exact opposite order to get them to display on the front end the way I would expect.
using WP_Query('posts_per_page=-1&post_type=section&orderby=menu_order&order=ASC....
While the top level parent pages seem to respect the ASC the sub-pages don't seem to.
Menu screenshot:
http://screensnapr.com/v/dNB1Ff.png
Front end:
http://screensnapr.com/v/zUaswC.png
notice the sub-pages offset