I am not as much an expert (actually, I am here to get an easy question answered myself ) but as far as I understand ROOT does a modification of a object already created and drawn on the screen imply, that the existing picture of the object itself is modified - upon the next Update().
So when you are adding a second graph to the existing multigraph and draw the same multigraph again, it will show identical graphs in both pads.
Your intension, however, was to show only the first plot in the first pad (different pictures). To do so, I would copy the multipad with the Clone() method before adding the second Graph.