During developing web using Drupal 7, sometimes we caught with duplication of menus when using Admin Menu. This problem usually happen when we accidently move or modify administration menu to other menu blocks. Actually it shoudn't happen because Drupal was designed to able handle any modification make to any menu.
However when someone with inexperience with Drupal system, installing unstable modules that interfere with Drupal menu system could leads this problem happened unexpected.
We need to log into database either through bash or using GUI like PHPMyAdmin.
Then, ran this query:
DELETE FROM `menu_links` WHERE `menu_links`.`module` = 'admin_menu'
After that ran this query:
DELETE FROM `menu_links` WHERE `menu_links`.`module` = 'system'
These two query will delete all menus under admin menu. You will face blank menu if try to refresh any page.
After that go to "admin/build/modules".
Here Drupal will rebuilt all menu system again based on default configuration.
If it still didn't work, repeat this step again but instead go to "admin/build/modules", run directly in web browser bar, "http://example.com/update.php". This step will force Drupal to refresh all default configuration and modules installed.
Lastly clear all Drupal cache manually.