In planes, pedals control the rudder, which controls bank rate of aircraft.
Yoke motion from side to side affects ailerons, which control the roll of aircraft. And forward-backward youke motion controls the elevator(s), which control pitch. This is a natural set-up in planes, since turning always involves manipulation of all control surfaces. First you roll to direction you want to turn, then apply rudder to that direction so that the fuselage stays about straight in the airflow, and during the roll you also want to use the elevator to increase the angle of attack of wings to counter the loss of lift caused by rolling.
Rudder is used because in a turn, the outer wing naturally travels faster than the inner wing. Greater speed causes greater drag, so there appeares a force that banks the plane out from the turn center... this force is countered by applying the rudder ever so slightly. This is called a controlled turn, and it's the most difficult thing in flying itself to get the rudder action right so that the plane goes straight in the airflow at any time. Make incorrect rudder movements and the plane flies sideways, which causes significantly more drag than flying straight. And make too fast rudder movements and you'll find the plane's nose oscillating from right to left... If you get the opportunity, go and take a glider flight. I learned a lot about flying on two flights I made last autumn.
However, in space sims it's usually easier (and traditional) to switch the roll and bank axis. That results in more intuitive control with a twist-handle joystick. There's no need to such complex maneuvering in vacuum, you just turn and accelerate and decelerate. It doesn't matter which way you're moving, it's always "forward".
Anyway, it's very weird if a configuration works in The Babylon Project and not in Freespace Open, because they are after all the same game.
What build are you using in TBP? And what in FSO?
