You can try to determine the mouse position by Java:
MouseInfo = java.awt.MouseInfo.getPointerInfo();
Pos = MouseInfo.getLocation();
x = int32(Pos.getX());
y = int32(Pos.getY());
This is in screen coordinates and the conversion to the coordinates of the axes is not trivial. But the problems to identify the clicks on the uicontrol's reveals a general problem with your approach: It seems to be a design mistake, that the zoom function reacts to clicks on buttons. Either zooming is triggered by the ButtonDownFcn of the axes only, or it is unintuitive, because the user cannot know, which parts of the figure are allowed to start the zooming. Think twice if your current approach (using the WindowsButtonDownFcn ?) is really the direct solution of the job.