"Um, don't run windows on critical systems on an airplane? (semi-serious)"
I'm not semi-serious! Running Windows for something like this is madness, absolute madness. Normally for critical systems in something like an airplane (i.e. *actually* critical, not "mission critical" like "oh my E-Mail is mission critical"...), they don't even consider Linux reliable enough, and it's FAR more reliable than Windows. There are specialized OSes for this kind of thing, like Green Hills Integrity OS.
"Just reading this it looks as though the safety of the plane depended on a central computer. Surely a plane has a log book that pilots should look at."
RTFA please. There were 2 faults logged the previous day, apparently they wait until 3 faults before not permitting a plane to take off.
In my view though, there were 2 causes for this: 1) Pilot error, since they didn't check the flaps. 2) Gross negligence on McDonald Douglas' part. They can try to blame the maintenance guys if they want. I'd assume some PC got a trojan, then in transferred to a diagnostic "box" they plug into the plane periodicially, then from there to the plane. But when going from a "PC" to a tool or embedded system, one should simply not have to worry about trojans and viruses -- as a tool or embedded system they don't need the flexibility of a full PC so they should not run random executables. The on-plane computer should absolutely never haphazzardly run executables, it should be running a high-reliability real time OS. The diagnostic box should be running something more reliable too, and really the PC should too, but they are at least not flight critical.