Some Drupal themes provide their own menu system instead of Drupal's built-in primary links menu. When enabling these fancy menus, your Drupal site may end up with two menu systems instead of one. In order to get rid of the primary links menu, you need to disable it:
- Log in with “administer menu” privileges.
- Navigate to to administer » settings » menus (admin/settings/menu) and set ‘Menu containing primary links:’ to ‘No primary links’. Repeat for the secondary links.