Now that's something I haven't heard of before, so does this happen with all the aircraft you fly? (ofcourse aircraft that have flaps at all)
the only thing I can suggest is
-have you tried mapping the flap keys to different buttons on your keyboard/Joystick to see if that solves the problem?
-Apart from your keyboard, mouse and Joystick do you hav any other 3th party controller that might cause a conflict?
HunterICX