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
options.Get(options::kFullScreenable, &fullscreenable);
  SetFullScreenable(fullscreenable);
  if (fullscreen) {
    SetFullScreen(true);
  }
  bool skip;
  if (options.Get(options::kSkipTaskbar, &skip) && skip) {
    SetSkipTaskbar(skip);
  }
  bool kiosk;
  if (options.Get(options::kKiosk, &kiosk) && kiosk) {
    SetKiosk(kiosk);
  }
  std::string color;
  if (options.Get(options::kBackgroundColor, &color)) {
    SetBackgroundColor(color);
  } else if (has_frame()) {
    
    SetBackgroundColor("#FFFF");
  }
  std::string title("Electron");
  options.Get(options::kTitle, &title);
  SetTitle(title);
  
  bool show = true;
  options.Get(options::kShow, &show);
  if (show)
    Show();
}
void NativeWindow::SetSize(const gfx::Size& size, bool animate) {