Its because of the dead battery, i'm guessing this is a 1.4 petrol. Need to give the battery a full charge and then let the car tick over for 30 minutes.
Just what a2steve said above, also if you got vcds or other scanning device that has got a function called "actuator test", just run that, it cycles through a few things, including pedal positions or something similar, which right away had fixed the same issue I had after flat battery.