It's most likely htaccess files throwing stuff off. Can you verify if there's a .htaccess file in both root and /joomla? Make sure you've enabled "Show Hidden Files" in your FTP program.
To get the /joomla part to work, use this wiki article for getting /stats to work. It works on the same principle:
To get WordPress to work, it's most likely a matter of getting its .htaccess in order.