http://ipaddress/~username

Hiyas. Im wondering if i can have a little help. For some reason if i usee http://ipaddress/~username this works (however it changes the Ip based url to a http://sub.domain.net/~username) Now if u click on a link to.. say /folder it goes to http://sub.domain.net/folder Missing out the username.. and displaying the 404 message used on this sub domains account. i have checked httpd.conf and this sub domain (for some reason) is the first virtualhost listed in apache. How would i go about preventing it from changing the IP address into a damned subdomain?? lol

Many thanks in advance