When I type in the servers ip address or an non existing subdomain I get a site that is on my server. This is a new site created on the 3.0.4 version. What can be the issue?
Thats the normal behaviour of the apache webserver. When you use the IP address to access a server and no website with that domain exists, then apache will deliver the first vhost in alphabetical order that it finds for this IP. It might be that you got a different website before the update as ISPConfig uses now a prefix for the vhost files. To show the website again that was shown before the ispconfig update, edit that website in ispconfig and change a value, e.g. quota and hit save, so that ispconfig reconfigures the vhost file for that website too.