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
#if defined(USE_X11)
  bool resizable;
  if (options.Get(options::kResizable, &resizable)) {
    SetResizable(resizable);
  }
#endif
#if defined(OS_WIN) || defined(USE_X11)
  bool closable;
  if (options.Get(options::kClosable, &closable)) {
    SetClosable(closable);
  }
#endif
  bool movable;
  if (options.Get(options::kMovable, &movable)) {
    SetMovable(movable);
  }
  bool has_shadow;
  if (options.Get(options::kHasShadow, &has_shadow)) {
    SetHasShadow(has_shadow);
  }
  bool top;
  if (options.Get(options::kAlwaysOnTop, &top) && top) {
    SetAlwaysOnTop(true);
  }
  
  bool fullscreenable = true;
  bool fullscreen = false;
  if (options.Get(options::kFullscreen, &fullscreen) && !fullscreen)
    fullscreenable = false;