Hi,
we're using moodle 2.2.4 at the moment and we've installed some cusom themes of our own. We can select these for the main site theme from Settings > Site Administration > Appearance> Themes > Theme selector but when we try to allocate them for individual courses using Settings > Edit settings the names of the themes are not visible in the drop-down menu next to Force themes.
We've set our moodle up to allow course themes in the theme settings and all of the theme language files have been re-named.