Keep in mind that most controls are just linked to the keyboard; there is no feedback between PC and controls concerning the initial positions of the controls and the start-up control settings of the sim. Therefore, it often happens that parking brake, lights and gear positions between sim and hardware do not match. (depending how you start your sim, from parking or at runway / mid-flight.
In Flight Unlimited III this can be easily corrected by pressing Escape (provided in the small keypad) and then returning to the sim by moving one of the levers. The lever movement will only be registered as a "back to sim" keystroke, but will not alter the sims cockpit settings. Repeating this sequence for the other mismatched controls will have quickly have you back with fully matching controls.