Ok I have some problems and questions

[joximu]

@rsmithgs:
Hm, the FQDN does not show up in the apache config - only if you choose the admin-URL to be the same as the FQDN - but I think rgenereting the config files won't change the 00_master.conf.
You have to change all by hand:
evtl. 00_master.conf, the postfix: main.cf, the proftpd.conf and maybe more (just don't know by hard).

Best would be to give the right host name during installation of *debian*, then the ispCP installation works too :-)

@samducker:
you *can* also use ns1.stra... as fqdn. Just to satisfy the rule so that you can use the domain name as a virtual host.

Normally you give the server a name (just the same as to your kids :-) and add the domain name after it. This will lead to e.g. superman.domain.com, mylinux.imthebest.net or whatever.
Of course: the hostname must be resolveable, so you have to add it in the DNS. And: to finish the whole story: add the FQDN also as the Reverse Lookup name for the server ip!

Please read some documentation about DNS and other important protocols/rules in the internet...

Cheers
Joximu