The fundamental issue here was the pilot's confusion over what was being reported to him by the plane's brains. I think it will be a long time before FBW aircraft and human pilots learn to live with each other without problems.
In the old days, a pilot (ususally) had an understanding of the mechanics, or physical elements, of the aircraft. The instrumentation was analog and the tactile feel was real. Today, with flat panel screens and computer genereated "feel", it is very easy for a pilot to fall out of the loop. On top of that is the fact that most people, pilots included, still have some level of scepticism when it comes to believing a computer. The result of this scetpicism is that, when the computer reports an event that seems to be really unbelievable, the pilot may spend an innordinate amount of time trying to disprove the computer rather than believe it right away. This scepticism is further fed by the fact that many "faults" can be eliminated by recycling circiut breakers, proving to the pilot that electronics are flaky and are not to be trusted. It is the Boeing and Airbus equivilent of the "blue screen of death" on your PC. We have been programmed to believe that a reboot fixes most problems.
Another element is the pilot's ability to understand programming logic as opposed to a mechanical function. It is one thing to understand how all of the fuel pumps and tanks interact. It is quite another to understand how the computer that controls the fuel system collects data, interprets the data, reports on the data, and acts upon the data. When faced with a problem that appears to make little sense, the pilot is forced to conceptualize what the computer is thinking. Unfortunately, pilots are not usually programmers. We now have a cyborg middleman between the pilot and the physical aircraft. Until the programmers develop a system that allows the cyborg and the human to think as one, these occasional "holes in the system" will continue to emerge. Let's hope that, as in this case, the human has the capacity to overcome the disconnect.