I was having the same problem (using rudder pedals would cause crash on takeoff).
I found an issue with the settings where the wrong controls were mapped to the brakes.
Settings->Other Settings->Controls
Select Control Axis tab
Controller type: Saitek Pro Flight Rudder Pedals (or eq)
Event->Brake (left axis) double click
Press Left Toe (on pedals) then OK to select. For some reason on mine it was selecting ailerons.
Same with the Brake (right axis). On mine that was selecting elevator axis?
see attached screen shot
Mike