There has to be something wrong with the server because now, when I create a new website, when I type the domain address in my browser I end in the /var/www forlder instead of the domain folder.
Ok, then you dont have a problem with php, you access your sites not trogh their vhosts. Instead you access them now trogh the global vhost.
Either you installed any software package which chnaged the global vhost of your linux distribution or something in dns has been changed.
To fix this, make sure that you selected the correct IP addresses for the websites in ispconfig instead of *