there is always the possibility that the wiring of the plane was somehow incorrect, connecting one system to the wrong circuit breaker
I doubt this, but have to throw it out there.
again, the plane seems to have crashed because the slats/flaps were not set properly for takeoff.
not because the warning system didn't work, though that might have saved them.
there are few things a pilot has to do before takeoff..and flaps is right up there with the most important of things.