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

content/shell/shell_content_browser_client.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 "content/shell/shell_content_browser_client.h"
 
 #include "base/command_line.h"
 #include "base/file_path.h"
 #include "content/shell/shell.h"
 #include "content/shell/shell_browser_main.h"
@@ skipping 245 matching lines @@
     bool worker) {
 }
 
 void ShellContentBrowserClient::CancelDesktopNotification(
     int render_process_id,
     int render_view_id,
     int notification_id) {
 }
 
 bool ShellContentBrowserClient::CanCreateWindow(
+    const GURL& opener_url,
     const GURL& origin,
     WindowContainerType container_type,
     content::ResourceContext* context,
     int render_process_id) {
   return true;
 }
 
 std::string ShellContentBrowserClient::GetWorkerProcessTitle(
     const GURL& url, content::ResourceContext* context) {
   return std::string();
@@ skipping 72 matching lines @@
 #endif
 
 #if defined(USE_NSS)
 crypto::CryptoModuleBlockingPasswordDelegate*
     ShellContentBrowserClient::GetCryptoPasswordDelegate(const GURL& url) {
   return NULL;
 }
 #endif
 
 }  // namespace content