You probably picked up a wrong VI, or miscalculated the coordinates.
To change the shape of the window, you've to define an opaque region. For single elliptic window, you can use "Window - O.vi". For complicated window, use "Combo Window.vi".
It probably has some coordinate-convert involved. It'll be easier to put your window at top-left corner of the screen for the first try.
George Zou
http://gtoolbox.yeah.net
George Zou