CiviCRM Upgrade from 4.5beta6 to 4.6.8 - CiviCRM Menu is not displaying/functioning
Its a core issue, civicrm/css/navigation.css doesn't gets loaded if drupal already has navigation.css loaded.
Check if your custom theme has navigation.css included, this would cause the error for menu not getting displayed 

Fix includes in https://issues.civicrm.org/jira/browse/CRM-17234

HTH
Pradeep