I'm ready to be accused of being simplistic, although I am only training for my ATPL. However... isn't it all a bit obvious? Even I know that flight with large bits of metal and rubber extended aren't going to help your fuel consumption. I find it utterly amazing that the pilots concerned tried to blame the FMS! It sound like utter complacency to me.
Wouldn't a simple "gross error check" have identified the problem quite early on?