Administration menu has gone wacky

did you try clearing caches, inc. varnish cache if there is one? If necessary turn off css aggregation too, and use a different browser just to be sure!

I am having the same issue. Just upgraded a simple site from D6 to D7 and the first thing I installed was Admin_Menu through Drush and my menu is all messed up. Tried clear cache, login/logout, turned off css aggregation and also tried both Firefox and Safari and get the same results.

I upgraded to the latest dev version of admin_menu and I am still seeing the same issue.

I was also seeing this problem on an upgraded site.
After some tracing I found that the 'management' menu was askew.
This link shows how to fix it: http://drupal.org/node/1123892
ie run
DELETE FROM menu_links WHERE module = 'system'
then clear the cache

That process help cleared my problem except that I had to modify it to be:
DELETE FROM drupalmenu_links WHERE module = 'system'

Thanks. I had the same problem and the SQL snippet fixed it.

So, how to deal with this?

Maybe a function like the following should be added in admin_menu.install?

<?php
function admin_menu_update_[num](){
  db_delete('menu_links')
    ->condition('module', 'system')
    ->execute();
}
?>

I also got this problem on Drupal 6 and the SQL query that worked for me is this.

DELETE FROM menu_links WHERE `menu_name` = `admin_menu`

then I clear the cache.

Having the same problem. The db_delete() did work, but only until the next cache refresh.
[EDIT] Also, db_delete() ruines my TaxonomyMenu and my main menu.
When running update.php, the following message appears, so that is pretty clear:
"Unresolved dependency System (Version >7.10 required) Administration menu requires this module and version. Currently using System version 7.9"

I will revert to my working dev-copy of 2011-05-06.

Upgrading the priority. At least a notice on the project page would be nice.

#1216714: Many bogus top-level links (especially after upgrading from Drupal 6)

taking away the image link as it shows an X and not the image.