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
SetBounds(gfx::Rect(GetPosition(), size), animate);
}
gfx::Size NativeWindow::GetSize() {
  return GetBounds().size();
}
void NativeWindow::SetPosition(const gfx::Point& position, bool animate) {
  SetBounds(gfx::Rect(position, GetSize()), animate);
}
gfx::Point NativeWindow::GetPosition() {
  return GetBounds().origin();
}
void NativeWindow::SetContentSize(const gfx::Size& size, bool animate) {