Ignore fullscreen windows which are behind other windows for fullscreen mode.

ash/root_window_controller.h

Index: ash/root_window_controller.h
diff --git a/ash/root_window_controller.h b/ash/root_window_controller.h
index 076bfe6a4f82e080f4b229131f53cd9c45148102..a171ffda01c3ca07227cd1671208c7e1a31d0f33 100644
--- a/ash/root_window_controller.h
+++ b/ash/root_window_controller.h
@@ -221,10 +221,10 @@ class ASH_EXPORT RootWindowController : public ShellObserver {
   // Initialize touch HUDs if necessary.
   void InitTouchHuds();
 
-  // Returns the window, if any, which is in fullscreen mode. If multiple
-  // windows are in fullscreen state, the topmost one is preferred.
-  const aura::Window* GetTopmostFullscreenWindow() const;
-  aura::Window* GetTopmostFullscreenWindow();
+  // Returns the topmost window or one of its transient parents, if any of them
+  // are in fullscreen mode.
+  const aura::Window* GetWindowForFullscreenMode() const;
+  aura::Window* GetWindowForFullscreenMode();
 
   // Activate virtual keyboard on current root window controller.
   void ActivateKeyboard(keyboard::KeyboardController* keyboard_controller);