Very basic version, some of which is supposition. The company's computerised maintenance recording system would throw up a warning if the same problem had been recorded for the same airframe on three separate occasions. In this particular case a sensor unit on the nose oleo of the aircraft had been shown to be faulty on two previous occasions.
The sensor reads whether the nose oleo is extended or not. Several different things are dependent on this sensor; the heating elements in the probes; and the takeoff configuration warning is another. In the first the heating elements are turned on when the sensor senses the nose oleo has extended on rotation otherwise they risk burning out on the ground without the airflow to cool them. In the second the takeoff configuration warning is silenced when the sensor senses the oleo has extended as the aircraft has rotated and obviously airborne and therefore a takeoff configuration warning is not required.
On the day of the flight the crew were taxying for takeoff when they became aware that the probes were overheating and they returned to the ramp for the engineers to address the problem. It was found that the nose oleo sensor had failed (this is now the third time on this airframe) and I believe the decision was made to depart with the sensor not working. The crew were to turn the heating elements on after takeoff.
In the rush to depart the now delayed flight the setting of the flaps for takeoff was overlooked. Because the nose oleo sensor was not working the takeoff configuration was also disabled (it thought the aircraft was in flight) and so the crew had no warning of their oversight.
That the maintenance computer had a virus (which I believe disabled the third warning) had no part to play in the crash. The third occurrence of the particular problem was on the day of the crash and the computer was not necessarily updated daily.
I think this crash is one of those perfect examples of Dr Reason's swiss cheese analogy at work. It goes to show that you need a good working knowledge of your systems and not to be distracted in your checks.