I also had this problem (on WP 3.5.1), but solved it by:
Network Settings -> Upload Settings -> Upload file types: add "css js", making it read something like "jpg jpeg png gif mp3 mov avi wmv midi mid pdf css js"
Then forced generation of the CSS and JS files by simply changing one of the CSS files (e.g. various.css) in [My Site] -> Appearance -> Montezuma Options.
All the best!