Thanks for the feedback, Michael.
We wound up reverting back to 3.6.0 as the easiest short term solution, and I haven't had a chance to test it any further yet. Will try to remember to check back in here with more info when that happens . . .
FWIW - I've been using multiple UIRoots with multiple UICameras to implement different sections of a UI since I first started working with NGUI, and have never noticed any trouble with it until now. I was under the impression that the culling mask and event mask settings made that okay, and never realized it was a questionable practice.
And now that I think of it, we just added a third party minimap plug-in that features NGUI integration, and the plugin uses its own UIRoot and UICamera as well. So it seems like maybe it would be a good thing for multiple UICameras to continue to play nice together going forward. Will get you some more information towards helping to make that the case, as soon as time allows.