I am running into the following error on a clean install of WordPress 3.5 using a network setup.
When I open Settings > Domains I see the following error:
Warning: Creating default object from empty value in /var/www/wordpress/wp-content/plugins/wordpress-mu-domain-mapping/domain_mapping.php on line 214
I assume because of the error or related it is failing to add any new domains to the mapping list.
http://wordpress.org/extend/plugins/wordpress-mu-domain-mapping/