There's a mistake I've made which a few others have made too. The mistake is rushing into your new Drupal site and populating your menu right away. You simply add new menu items as placeholders until you can create or add the data. You set the menu path to something like <front>, and populate away.
The frustrating part about this, is that your menus may not work as expected - at least when expecting cascading menus using the Primary links (or any other menu) as a hierarchy. Drupal needs to have something to point to in order to build it's internal menu.
There is an option within the Devel module to flush the menu (internally known as the menu router and menu links), and this is great to know, but won't help unless the menus are linked to actual content.
This video will walk you through the 'know-how' about how the menu works internally, and how to avoid the pitfalls of making your menus do what you want. I cover three other add on modules which you can use to make your Drupal serve up the order you've placed for it (did you catch that one? - if not, do you need a Menu? - being addicted keeps you crazy.)
- Menu block [issues] - [usage]
- Nice Menus [issues] - [usage]
- Menu Trails [issues] - [usage]
- Devel module [issues] - [usage]