I found this issue with MEPIS too, and I find it annoying! The default root directory for Apache is /var/www/apache2-default rather than just /var/www, which means all pages on my box are mybox.com.au/apache2-default/page.html. I've checked through Webmin and also /etc/apache2/apache2.conf and can't see this dir listed anyway. How do I change it?