I believe the manoeuvre margin floats on the dynamically computed red bricks (stall marker) and, as such, will vary with angle of attack (and other factors). The flap markers are simply Vref + xxkts. I assume the flap markers represent, well, not worst case scenario, but an airspeed value seen on test flights over a specific range of AOA's.
I've heard of instances on the 744 where a green flap marker has been been below the manoeuvre margin. A faulty Capt's or F/O's AOA vane has given a higher than normal stall value (and subsequently incorrect higher manoeuvre margin).
I stand to be corrected
