Use a hosted app's opener URL and not its origin to locate it.

content/shell/shell_content_browser_client.h

 // 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.
 
 #ifndef CONTENT_SHELL_SHELL_CONTENT_BROWSER_CLIENT_H_
 #define CONTENT_SHELL_SHELL_CONTENT_BROWSER_CLIENT_H_
 #pragma once
 
 #include <string>
 
@@ skipping 120 matching lines @@
   virtual void ShowDesktopNotification(
       const content::ShowDesktopNotificationHostMsgParams& params,
       int render_process_id,
       int render_view_id,
       bool worker) OVERRIDE;
   virtual void CancelDesktopNotification(
       int render_process_id,
       int render_view_id,
       int notification_id) OVERRIDE;
   virtual bool CanCreateWindow(
+      const GURL& opener_url,
       const GURL& origin,
       WindowContainerType container_type,
       content::ResourceContext* context,
       int render_process_id) OVERRIDE;
   virtual std::string GetWorkerProcessTitle(
       const GURL& url, content::ResourceContext* context) OVERRIDE;
   virtual void ResourceDispatcherHostCreated() OVERRIDE;
   virtual SpeechInputManagerDelegate* GetSpeechInputManagerDelegate() OVERRIDE;
   virtual ui::Clipboard* GetClipboard() OVERRIDE;
   virtual net::NetLog* GetNetLog() OVERRIDE;
@@ skipping 28 matching lines @@
           const GURL& url) OVERRIDE;
 #endif
 
  private:
   ShellBrowserMainParts* shell_browser_main_parts_;
 };
 
 }  // namespace content
 
 #endif  // CONTENT_SHELL_SHELL_CONTENT_BROWSER_CLIENT_H_