I too am having a similar issue, I have gameObjects I want to click on, that all works, I can tell what I am clicking on and store the objects, however if I click on an NGUI element, it behaves as though I am clicking on another object from the main camera. I realize why this is (mousepick is sending a raycast from main cam, not the UI cam.) But how can I get around this? Making the UI camera follow the main cam would work technically, but its sloppy and wont help with UI scaling.
Any help would be great.