I really don't know why this happen.
Some more information that could be important:
The "domain.de" Domain is added as an alias domain to an customer account in i-MSCP and "ns1.domain.de" and "ns2.domain.de" are the nameservers that i'm using for all domains. When I enter these into the listener file and run the setup, apache won't start anymore. When I delete these two nameservers from the listener file and run the setup, everything works.
Like I said already, i removed the listener file and edited the bind template manually, like all the versions before, so everything works on my server now. But with the listener file it would be a bit easier and the changes won't be deleted when updating i-MSCP.
I know that my nameserver setup is little bit weird at the moment. I'm working on it to get an extra domain only for "ns1" and "ns2" without creating an i-mscp customer and so on.