Symptoms

When logged in as a user with administrative privileges, clicking the Administration link results in the Projects admin page showing but all of the links in the navigation bar at the left missing. If JIRA Agile (GreenHopper) is installed, its administration settings will be showing, but not others. Going directly to a particular admin page by entering the URL manually works.

Cause

Earlier versions of JIRA allowed users to disable the Admin Menu Sections plugin, which is what displays the Administration links. Even under more recent versions of JIRA where it's not possible to disable the plugin, if a backup from an older instance is imported where the plugin was disabled, it will be disabled after the data is restored.

Resolution

Go directly to the URL that enables the Admin Menu Sections plugin:

http://<baseurl>/secure/admin/jira/ViewPlugins.jspa?mode=enable&pluginKey=jira.webfragments.admin

Replace <baseurl> with your URL

Once visited, the admin menus will be displayed again.