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
brightray::InspectableWebContents* inspectable_web_contents,
    const mate::Dictionary& options)
    : content::WebContentsObserver(inspectable_web_contents->GetWebContents()),
      has_frame_(true),
      force_using_draggable_region_(false),
      transparent_(false),
      enable_larger_than_screen_(false),
      is_closed_(false),
      has_dialog_attached_(false),
      aspect_ratio_(0.0),
      inspectable_web_contents_(inspectable_web_contents),
      weak_factory_(this) {
  options.Get(options::kFrame, &has_frame_);
  options.Get(options::kTransparent, &transparent_);
  options.Get(options::kEnableLargerThanScreen, &enable_larger_than_screen_);
  
  
  ui::GpuSwitchingManager::SetTransparent(transparent_);
  
  options.Get(options::kIcon, &icon_);
  WindowList::AddWindow(this);
}
NativeWindow::~NativeWindow() {