I found that after upgrading from 6.x-1.8 to 6.x-3.0alpha4 I had all of my admin menu items listed twice (see attachment) I made sure the navigation block was hidden/disabled like it says in the readme. After flushing the cache numerous times and tweaking menu settings I finally decided to look into the database. I ran
DELETE FROM `database`.`menu_links` WHERE `database`.`menu_name` = "admin_menu"; followed by
drush cc all which regenerated the admin menu links and this time there were the proper amount.