Thank you Robertson.
That was the exact problem. For some reason, the Centrify-enhanced OpenSSH was the problem. I am not sure what happened. After removing it from the system, I was able to re-establish my connection to all my machines via SSH.
The funny thing is, using the Centrify Deploy Manager to push out the update from an older version is actually what broke everything.
One would think, if it is able to connect to the machines via SSH - authenticate, update and so on, that afterwards, it would be able to configure the OpenSSH the way it should be set. But unfortunately, for some odd reason, it doesn't. And I could not find where to tell it to not "disable root" login via ssh.
Strange. But all is well.
Cheers.