After further examination I think I have come up with an explanation about the weird behaviour exhibited by the a/c on this "maiden" flight.
It was a ProPilot flight, the server did not take notice of it but that is beside the point of this thread. However, my local FlightLogger client DID grey out the ProPilot button, so as far as it was concerned it WAS a ProPilot flight. The server does not program failures (or it may), it is the task of Flight Logger (which actually connects to FS) to generate these faults at random times. Pretty interesting if you think about it.
The ProPilot system introduces "a complex algorithm for aircraft failures based on the amount of hours accumulated before a maintenance cycle".
My a/c was not so "virgin" and I guess I was given some failures to keep me entertained

[as it indeed was]. Under normal circumstances this would not be the case as I had flown it manually before.
I recall that sometime during the beginning of the flight there was a mention of "aircraft has been damaged" and hell broke lose at random afterwards.
Some of the causes of the weird behaviour are the windshear encountered with the "real weather" at that time but mostly due to the random failures programmed by FlightLogger in the PP algorithm (as expected).
The behaviour exhibited by the a/c during the "extreme circumstances" seem to be in accordance to some failures I experienced before with a "damaged" aircraft using the FS Passengers trial add-on as well as with the rudder getting stuck either left or right or ailerons getting stuck. The latest also consistent with failures I have seen described in Discovery Channel/National Geographic "Aircraft Crash Investigation". One of those rudder failure episodes was actually on TV just last week if I remember correctly.
And the "horrendous experience" was not mine -I think there has been a misunderstanding there-, it was experienced by the virtual passengers on the flight.
If you haven't experienced those failures then lucky you

yet at the same time you have certainly missed the oppty. to attempt to handle these situations, luckily mine didn't crash.