Duplicate Entries in Administration Menu

Hello,

I have just upgraded to the 3.0-alpha3 version. Now when I look at the menu all the headings are duplicated.
This is what I see:
[***** Horizontally *****]
* Home [Drupal Logo]
* Home [Drupal Logo]
* Log out @username
* Create content <-- This only appears ONCE
* Content management
* Content management
* Site building
* Site building
* Site configuration
* Site configuration
* User management
* User management
* Reports
* Reports
* Help
* Help

I had an issue when I first updated, I was getting an error saying that an admin menu cache table was missing. I disabled the module then did an uninstall through the Drupal interface. After that I deleted the "admin_menu" folder from my sites/all/modules folder. I then recopied the folder and enabled the module in Drupal modules screen.

I did a database update and flushed all caches. The error about the missing table is gone, but all the entries appear twice now.

Any help would be greatly appreciated. Thanks.