Hi,
I am having the same problem here (or the effect seems the same), and using different layers is not really an option.
What I am trying to do is cross fade two scenes the current and the newly (additive loaded scene)... The type of transition could get more complicated assuming I can find a way around the rendering problem.
I say using layers is not an option since I have potentially a lot of these screens and having a layer per screen would not work...
I get a rendering artefact in my case once I remove the old scene (DestroyObject), what I have found is that once it goes wrong, if I disable/enable (from the inspector) the root then things go back to normal..
In my case I don't need to have these active at the same time (aside from the transitioning), is there some way I can achieve the transition I am after an play nice with nGUI. Maybe force an update after the transition is finished???
Cheers
Graeme