Since DS handles those objects by itself,  the system won't see them or handle them. As with luck would have it, the window manager will sometimes bug and crash, removing the title bar and therefore moving applications, including DS, upward by x amount of pixels, If this happens and DS gets terminated properly, the positions of the free-floating objects gets saved with wrong position. Next time you start DS you can't grab and position the offending window because the title bar has moved over the edge of the screen. This happens easily on dual screen computers where the secondary screen is positioned left of the primary screen.

How do I reset position of the properties window (see image)?