Unity in editor mode with active 'SceneView' and hidden 'GameVeiw' always report Screen.width and Screen.height as 640x480. Camera.pixelRect also return rect with the same size. Camera.ViewportToWorldPoint and Camera.ScreenToWorldPoint return result for 640x480.
You can see this problem in video:
https://www.youtube.com/watch?v=_CqKkphYflEAs result, in 'Scene view' you have different NGUI UI image, not the same as GameView.
To fix this behaviour, I made changes in NGUITools.cs, UIRoot.cs and UIAnchor.cs (see attached NguiWysiwig2.diff)
And I added AlignCameraToUI - it's constraints 'Scene View' camera to UI bounds and give you exactly the same picture, as 'Game View'. You can Turn on/off it in menu "NGUI/Extras/Enable Align to camera to UI"
I hope to see similar changes in next releases of NGUI.
Sorry for poor english.