Yeah, I did the short URL's yesterday. Something like domain.com/Cla now gives me an error page within MediaWiki, but domain.com/Cla/jjg/kkj I get " The requested URL /Cla/jjg/kkj was not found on this server." If you look at www.wowwiki.com/Cla/jjg/kkj they still get the error page.
Sounds like a mistake in however you've done the short URLs - certain urls (ones with extra slashes, perhaps?) aren't getting passed to index.php. If you give the details of how you did the short urls (copy and paste the code you added and say what file(s) it's in) we might be able to help.