I think this would be a question for Unity as it's something to do with how Unity 5's new scene management works. If I understand you correctly, scene 2 is the one with the UI. Scene 1 has no UI, no UICamera, no UIRoot, nothing -- right? It merely loads the second scene? I can only suggest checking your cameras. If your first scene has a camera that clears color, make sure that the second scene does too, and that their depths are set to what you'd expect.