Found this issue on a project, tested against the electron-quick-start and found the problem still exists.

Simply adding "frame: false" to the new BrowserWindow() call will cause it.
- Electron version: 0.37.5
- Operating system: Windows

![capture](https://cloud.githubusercontent.com/assets/5051169/14453254/a38c177c-008b-11e6-9e80-97c6a95c816e.PNG)

atom/browser/native_window.cc
WindowList::WindowCloseCancelled(this);
  
  window_unresposive_closure_.Cancel();
}
bool NativeWindow::OnMessageReceived(const IPC::Message& message) {
  bool handled = true;
  IPC_BEGIN_MESSAGE_MAP(NativeWindow, message)
    IPC_MESSAGE_HANDLER(AtomViewHostMsg_UpdateDraggableRegions,
                        UpdateDraggableRegions)
    IPC_MESSAGE_UNHANDLED(handled = false)
  IPC_END_MESSAGE_MAP()
  return handled;
}
void NativeWindow::UpdateDraggableRegions(
    const std::vector<DraggableRegion>& regions) {
  
  if (has_frame_ && !force_using_draggable_region_)
    return;
  draggable_region_ = DraggableRegionsToSkRegion(regions);
}
void NativeWindow::ScheduleUnresponsiveEvent(int ms) {