In multisites, the Shibboleth menu appears under each individual site, and each site admin can make global changes to the shibboleth settings which are affecting all sites. This menu should be removed from individual sites, and inserted in its proper place, most likely in the Settings menu only visible to the network admin.

I found this possible solution:
http://wordpress.org/support/topic/shibboleth-plugin-needs-maintenance-help
which seems to work, but I'm not a WordPress plugin developer.

Here is a diff of the file wp-content/plugins/shibboleth/options-admin.php to modify:

< // begin changes
<   //add_action('admin_menu', 'shibboleth_admin_panels');
<   add_action( 'network_admin_menu', 'shibboleth_network' );
< function shibboleth_network() {
<         $hookname = add_submenu_page('settings.php', __('Shibboleth Options', 'shibboleth'),
<                 __('Shibboleth', 'shibboleth'), 8, 'shibboleth-options', 'shibboleth_options_page' );
< }
< // end of changes

---
>   add_action('admin_menu', 'shibboleth_admin_panels');

See more discussions in the support forum http://wordpress.org/support/topic/shibboleth-options-on-multisite-wordpress-installation