FYI, I have this exact problem as well. Unity 4.5.1p3, NGUI just updated via asset store, so I guess 3.6.6? In my case, NGUI works perfectly fine letting Unity auto-rotate the GUI. But when I programmatically change to:
Screen.orientation = ScreenOrientation.Landscape;
During normal user input handling, I get no more events from the UICamera when running in iOS.
So NGUI updates the layout to the new orientation. But events stop flowing to it. I do get them when running in Android. Everything seems fine there.
Anecdotally, the gyro input that I'm running in parallel (outside of the NGUI system) continues to work fine. So Unity itself isn't frozen. It's just the UI events that are not flowing.
I'm about to dig into this. But thought I'd confirm it as best I can.