If you look in the advanced options on the UIPanels that you're anchoring to, if "Offset" is checked, the position of UIRoot counts. An offset of 20,20 will move your stuff 10 screens away. It works on the global position of the panel. Quick fix is to place UIRoot in 0,0,0.
Also take a look at your layers. NGUI finds its cameras by looking at which layer the widget/camera is in, (FindCameraForLayer), so if you're using default for everything things like this can happen depending on which camera is found first. Move your UI into its own layer (define a new one) and see if the problem persists.