You dont have to use the ispconfig network configuration feature to use ispconfig. Noramally IP addresses are configured with the config tools of the operating system directly, thats why the ispconfig network config is disabled by default and leving it off is the recommended setting.
So in your case, disable the network configuration option in ispconfig again and add the IP addresses with the ubuntu network configuration utility instead.
My question is, why now my interfaces have the "dns-nameservers" missing ?
Normally the nameservers are set in /etc/resolv.conf, they dont have to be set in the interfaces file.