somebody recently told a story of 2 cloned vm machines, the same hardware and configuration. same updates installed on both. one did not start up correctly, other one runs smoothly.

windows platform is way more unpredictable then any other system i worked with.

I can't say I've every had that happen to me or anyone else I've dealt with. Do you have any references to relevant bugs/issues? A properly running package manager should not allow this unless there is a serious bug in the packages themselves.

The closest I can think of otherwise is someone getting locked out of a remote machine where root was the only active account and was authenticated buy user/pass not by key, and he accepted the "start blocking password logins for root" change in a distribution upgrade (so he was warned so his own fault!).

I've never had that happen, but thankfully remote (virtual) serial consoles are commonplace. Something I wish was more common in Windows environments, as I've had remote access dump on Windows many times, leaving me with no options other than a long drive or call in to a remote DC.