Problem dragging windows to second display

I have a second display arranged on top of my macbook air display. Everything seemed fine with Lion, but with Mountain Lion only some of the windows can be dragged vertically to the second display (e.g. excel) while others stop at the menu bar (e.g. safari).

However, when I arrange the displays horizontally I have no problem with any window. I can even rearrange the second display to the top and carry the problem windows with it. But if I then drag the problem windows down to the primary display I can't move then back up again.

Is there some preference setting for these open windows that is causing this behavor? Or is this a gilich in Mountain Lion itself?