In order to be changes to the settings after upgrading to WordPress 3.3, I need to edit the database directly through PHPmyadmin. This is happening on numerous multisite installs.
Permanent redirect (better for your blogger's pagerank)
User domain mapping page
Redirect administration pages to site's original domain (remote login disabled if this redirect is disabled)
Disable primary domain check. Sites will not redirect to one domain name. May cause duplicate content issues.