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
#include "atom/browser/native_window.h"
#include <string>
#include <utility>
#include <vector>
#include "atom/browser/atom_browser_context.h"
#include "atom/browser/atom_browser_main_parts.h"
#include "atom/browser/window_list.h"
#include "atom/common/api/api_messages.h"