i have the same problem here ... all sites go to /var/www.
in my case i found the error very quickly ... /etc/apache2/vhosts/Vhost_ispconfig.conf was empty.
i dont know how this can be.
There are some other files starting with "Vhost_ispconfig".
for example: Vhost_ispconfig.c~27-09-07_15-10-29
I think this file is a backup?
finaly i copied the latest file to Vhost_ispconfig.conf ... restart of apache puted out an error "php_admin_flag is unknown".
I deleted this row from Vhost_ispconfig.conf and the restart of apache2 was successful.
From this moment i get the correct site.
But: how it can be that Vhost_ispconfig.conf is empty??