Don't use command line flags for enabling the internal pdf plugin. Instead, ...

chrome/browser/dom_ui/plugins_ui.cc

 // Copyright (c) 2010 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 "chrome/browser/dom_ui/plugins_ui.h"
 
 #include <algorithm>
 #include <string>
 #include <vector>
 
@@ skipping 300 matching lines @@
 }
 
 // static
 void PluginsUI::RegisterUserPrefs(PrefService* prefs) {
   FilePath internal_dir;
   PathService::Get(chrome::DIR_INTERNAL_PLUGINS, &internal_dir);
   prefs->RegisterFilePathPref(prefs::kPluginsLastInternalDirectory,
                               internal_dir);
 
   prefs->RegisterListPref(prefs::kPluginsPluginsList);
+  prefs->RegisterBooleanPref(prefs::kPluginsEnabledInternalPDF, false);
 }