Hello, It seems the pathfinder in option bar and in property window are not the same.
If I create a rectangle on my layer with pathfinder on new layer (the selected color is in the new shape) and then select subtract in option bar pathfinder, the fill color moved outside the shape !!!!. If then I select the "add" pathfinder in the property window the fill color moved back in the shape. BUT the pathfinder in option bar STAYS in subtract mode !!.
It is as the property windows acts on curent path in layer and the option bar combines the path on layer and the new path added.