When you use the scrollbars within the context of an NGui DraggablePanel, the scroll bars move the clipping area around (I am assuming) so it will show and hide elements based on the scrolled position (or internal position if the scrollbars are just updating some internal position).
Either way the reason I mention the scroll bars is because I am drawing the lines where the element should be within the scene (also viewed through the debugger to check they are correct which they seem to be) but the elements appear elsewhere in the actual game so I am just wondering if given the above psudocode for drawing a line between 2 NGUI objects am I missing something which is specific to how NGUI operates? As I am still a novice at unity, so it can be a bit confusing when there is a main camera, and another camera in the NGUI part but this displays within the main camera anyway, so I could be missing a transform or some translation due to the way NGUI is rendered, especially when its being offset by a draggable panel with scrollbars.
So that is why I mentioned them, and was hoping someone who has more experience with NGUI/Unity would just see straight away where I am going wrong with the getting and assigning of the points to world space etc and just point me in the right direction.