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
UINT message, WPARAM w_param, LPARAM l_param) {
  FOR_EACH_OBSERVER(NativeWindowObserver, observers_,
                    OnWindowMessage(message, w_param, l_param));
}
#endif
scoped_ptr<SkRegion> NativeWindow::DraggableRegionsToSkRegion(
    const std::vector<DraggableRegion>& regions) {
  scoped_ptr<SkRegion> sk_region(new SkRegion);
  for (const DraggableRegion& region : regions) {
    sk_region->op(
        region.bounds.x(),
        region.bounds.y(),
        region.bounds.right(),
        region.bounds.bottom(),
        region.draggable ? SkRegion::kUnion_Op : SkRegion::kDifference_Op);
  }
  return sk_region;
}
void NativeWindow::RenderViewCreated(
    content::RenderViewHost* render_view_host) {
  if (!transparent_)
    return;
  content::RenderWidgetHostImpl* impl = content::RenderWidgetHostImpl::FromID(
      render_view_host->GetProcess()->GetID(),
      render_view_host->GetRoutingID());
  if (impl)
    impl->SetBackgroundOpaque(false);
}
void NativeWindow::BeforeUnloadDialogCancelled() {