jaytime. I think we just had the same problem. It was solved as follows:
1. Make sure your page orders are correct in the Manage->Pages->Page Orders fields e.g. /wp-admin/page.php?action=edit&post=7
The lowest number will appear on the left in your nav bar.
2. Then go to Presentation->[theme] options (at least it worked for us in Tarski). You’ll then see your list of pages that you want to include in the correct order. Click on Update Options and the change should be reflected in the site.
I expected it to be a one stage process in Page Orders but it was only after updating the theme options that it affected the site.