Hi,
i have the same pb with my wordpress 3.1.3 multisite instance using the latest version of the plugin and simplesamlphp v1.8.
saving the parameters only work for the root blog and not at all for the sub-sites, nothing is actually written in the db.
using firebug, you can see that form action url in the sub-sites admin configuration page points to the root blog.
regards, Jean