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
NotifyWindowClosed();
}
NativeWindow* NativeWindow::FromWebContents(
    content::WebContents* web_contents) {
  WindowList& window_list = *WindowList::GetInstance();
  for (NativeWindow* window : window_list) {
    if (window->web_contents() == web_contents)
      return window;
  }
  return nullptr;
}
void NativeWindow::InitFromOptions(const mate::Dictionary& options) {