Calls to GetLoginItemSettings (amonst others) will get GetAppUserModelId which will implicit set a new one if there hasn't been a user defined one yet.  This causes an issue in a UWP environment where the AppUserModelId is system defined.

On the latest versions of windows the AppUserModelId defined for your notification must match exactly the one defined for your process or no notification will appear.  Got a fix in the works for this just raising here for tracking purposes.
atom/browser/browser.cc
bool prevent_default = false;
  for (BrowserObserver& observer : observers_)
    observer.OnBeforeQuit(&prevent_default);
  return !prevent_default;
}
void Browser::OnWindowCloseCancelled(NativeWindow* window) {
  if (is_quiting_)
    
    
    is_quiting_ = false;
}
void Browser::OnWindowAllClosed() {
  if (is_exiting_) {
    Shutdown();
  } else if (is_quiting_) {
    NotifyAndShutdown();
  } else {
    for (BrowserObserver& observer : observers_)
      observer.OnWindowAllClosed();
  }
}
#if defined(OS_MACOSX)
void Browser::NewWindowForTab() {
  for (BrowserObserver& observer : observers_)
    observer.OnNewWindowForTab();
}
#endif
}