Affects Version/s: 4.6
Fix Version/s: 4.6.9
Funding Source:Contributed Code
CiviCRM menu does not get displayed if the theme has navigation.css file.
Drupal code(https://api.drupal.org/api/drupal/includes!common.inc/function/drupal_get_css/7) checks for filename in css array and unset duplicate css file name if any irrespective of file path.
Not sure if its a bad architecture by Drupal, it recommends to use unique file name i.e modulename_styles.css
add navigation.css in theme
i.e in theme.info add line
stylesheets[all] = css/navigation.css