OK, here's john's patch plus my sync stuff.

chrome/browser/ui/views/extensions/native_app_window_views.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 "chrome/browser/ui/views/extensions/native_app_window_views.h"
 
 #include "chrome/app/chrome_command_ids.h"
 #include "chrome/browser/extensions/extension_host.h"
 #include "chrome/browser/favicon/favicon_tab_helper.h"
 #include "chrome/browser/profiles/profile.h"
@@ skipping 103 matching lines @@
   // TODO(erg): Conceptually, these are toplevel windows, but we theoretically
   // could plumb context through to here in some cases.
   init_params.top_level = true;
   window_->Init(init_params);
   gfx::Rect window_bounds = create_params.bounds;
   window_bounds.Inset(-GetFrameInsets());
   // Center window if no position was specified.
   if (create_params.bounds.x() == INT_MIN ||
       create_params.bounds.y() == INT_MIN) {
     window_->CenterWindow(window_bounds.size());
-  } else {
+  } else if (!window_bounds.IsEmpty()) {
     window_->SetBounds(window_bounds);
   }
 
   // Register accelarators supported by app windows.
   // TODO(jeremya/stevenjb): should these be registered for panels too?
   views::FocusManager* focus_manager = GetFocusManager();
   const std::map<ui::Accelerator, int>& accelerator_table =
       GetAcceleratorTable();
   for (std::map<ui::Accelerator, int>::const_iterator iter =
            accelerator_table.begin();
@@ skipping 450 matching lines @@
 }
 
 //------------------------------------------------------------------------------
 // NativeAppWindow::Create
 
 // static
 NativeAppWindow* NativeAppWindow::Create(
     ShellWindow* shell_window, const ShellWindow::CreateParams& params) {
   return new NativeAppWindowViews(shell_window, params);
 }