FocusController needs to restack windows upon activation (but not focus).

ui/aura/window.cc

 // Copyright (c) 2012 The Chromium Authors. All rights reserved.
 // Use of this source code is governed by a BSD-style license that can be
 // found in the LICENSE file.
 
 #include "ui/aura/window.h"
 
 #include <algorithm>
 
 #include "base/bind.h"
 #include "base/bind_helpers.h"
@@ skipping 761 matching lines @@
                                              return_tightest,
                                              for_event_handling);
     if (match)
       return match;
   }
 
   return delegate_ ? this : NULL;
 }
 
 void Window::RemoveChildImpl(Window* child, Window* new_parent) {
-  Windows::iterator i = std::find(children_.begin(), children_.end(), child);
-  DCHECK(i != children_.end());
   if (layout_manager_.get())
     layout_manager_->OnWillRemoveWindowFromLayout(child);
   FOR_EACH_OBSERVER(WindowObserver, observers_, OnWillRemoveWindow(child));
   RootWindow* root_window = child->GetRootWindow();
   RootWindow* new_root_window = new_parent ? new_parent->GetRootWindow() : NULL;
   if (root_window && root_window != new_root_window) {
     root_window->OnWindowRemovedFromRootWindow(child, new_root_window);
     child->NotifyRemovingFromRootWindow();
   }
   child->parent_ = NULL;
   // We should only remove the child's layer if the child still owns that layer.
   // Someone else may have acquired ownership of it via AcquireLayer() and may
   // expect the hierarchy to go unchanged as the Window is destroyed.
   if (child->layer_owner_.get())
     layer_->Remove(child->layer_);
+  Windows::iterator i = std::find(children_.begin(), children_.end(), child);
+  DCHECK(i != children_.end());
   children_.erase(i);
   child->OnParentChanged();
   if (layout_manager_.get())
     layout_manager_->OnWindowRemovedFromLayout(child);
 }
 
 void Window::OnParentChanged() {
   FOR_EACH_OBSERVER(
       WindowObserver, observers_, OnWindowParentChanged(this, parent_));
 }
@@ skipping 153 matching lines @@
   bool contains_mouse = false;
   if (IsVisible()) {
     RootWindow* root_window = GetRootWindow();
     contains_mouse = root_window &&
         ContainsPointInRoot(root_window->GetLastMouseLocationInRoot());
   }
   return contains_mouse;
 }
 
 }  // namespace aura