I had a problem recent that looks a bit like this one. The "default" Vhost seems to block 1 site. This site had the domain the server itself had to host some general scripts and tools.
When I changed the FDN belonging to the public IP in /etc/hosts to a another domain the problem was gone.
So, dont try to host a site under the same domain as your server has, in my case it fails to server the content of the default Vhost.
Maybe its of use to someone searching for this.