piceagle, I have just realised what I think your problem is. You possibly have the switch action reversed, so the mixer thinks that flaps down is actually the up position. If you go into the controls assignment and reverse the action of the switch. (The * should show when the flaps are up.)
The mixer will then adjust the correct positions. you may have to reverse the flap servos in the servo calibrate menu to account for the revised switch direction.