Everything in the left column including the logo, link to the 'home' page and toolbox are not visible in the default (vector) skin. I doubt this is intentional since there is still content there; it's just hidden. When I login and set my preference to a different skin it works fine. I checked
http://directory.fsf.org/wiki?title=MediaWiki:Common.css for vandalism, but it's fine.
Since I know how to "skin" mediawiki, perhaps I can help.