We recently had problems with the server that hosted our JIRA installation. We needed to migrate the installation to a new server. After that migration, for some unknown reason most of the options that normally appear on the Administration page had disappeared.
I found a JIRA Knowledge Base article, Menus Missing from JIRA Administration Panel, that speaks of this phenomenon and how to fix it. The solution is to hit the following URL:
http://myjirahost/secure/admin/jira/ViewPlugins.jspa?mode=enable&pluginKey=jira.webfragments.admin
where myjirahost is the base of your JIRA installation.