I am using multisite 3.1, and I have the network plugin from wpebooks.com. I've created all the directories that needed created but the themes do not appear in my new network. Do I have to do something else besides create /wp-content/ms-themes/siteid?
http://wordpress.org/extend/plugins/multisite-themes/
Josh, are you creating a directory of "/siteid" or "/XX" where XX is the ID of the network?
Note that this is for themes per Network, not themes per site.
WordPress does themes per site on a fresh install of Multisite no problem.