Wrong CA certificate with new install

When I setup a new server for a new domain, it create a certificate with the following:
server
Univention Corporate Server Root CA (ID=xxxxxx) for the common name, instead of the server, or domain common name.

And when I create a new Certificate CA it didn’t update the /etc/simplesamplphp/ucs-sso.domainname.org…

This looks like http://forge.univention.org/bugzilla/show_bug.cgi?id=40229

The support article was not completely up to date. You should find the relevant information here, in the SAML SSO section: Renewing the SSL certificates