in both places? They are both the same domain.
It doesn't matter that both are the same domain. They are running with two different apache instances (the one for the system on port 80 and ispconfig's own on port 81) and are therefore technically two different sites. The second one (ispconfig's own) doesn't yet know anything about a new certificate. Copy the cert to the location Falko gave in his post and modify /root/ispconfig/httpd/conf/httpd.conf accordingly.