Updated to admin_menu-6.x-3.0-alpha3 and lost admin links. Then I 'fixed' it.

After this update, the Administer link disappeared from the navigation menu.

- On disabling admin menu module, my Administer link was restored.

- When viewing the admin screen, all my admin links had disappeared, apart from organic groups. And disabling or unistalling admin menu module did not fix this.

- It is possible that a server crash corrupted my menus somehow.

These are the steps I went through and in the end my admin links were restored; all this may not be necessary:

1. I uninstalled the latest version of admin menu module, and reinstalled the last working version (6.x-1.5).
2. Ran update.php a few times. This did not fix the main admin page, but the admin menu was restored correctly.
3. I checked on the menu configuration page: /admin/build/menu-customize/navigation. Couldn't see the links there (if you are looking - check all submenus - yours may be there).
4. I flushed all caches (using the admin menu - links below the drupal icon).
5. I used "Rebuild menus" link in my Devel module block.*** (see cron note below)
6. Ran update.php again.

After all this, I still did not have admin links visible on the screen.

Next day, I checked the menu configuration page: /admin/build/menu-customize/navigation. The missing admin links were visible as sub-menus of another item (Create content).
It's possible they were present before, and I didn't see them.

It's also possible that my overnight cron run reset things, and made them show up, following the menu_rebuild. Perhaps if I'd ***run cron manually*** it would have fixed immediately.

I have now put the menu items back in the order I want them.

I am not installing further admin_menu updates on my site until I know it is stable. The maintainers are working on this now - see: http://drupal.org/node/550254/#14

Also see this thread for more information... http://drupal.org/node/511744