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.h
std::string GetExecutableFileProductName() const;
  
  void NotifyAndShutdown();
  
  bool HandleBeforeQuit();
  bool is_quiting_;
 private:
  
  void OnWindowCloseCancelled(NativeWindow* window) override;
  void OnWindowAllClosed() override;
  
  base::ObserverList<BrowserObserver> observers_;
  
  bool is_exiting_;
  
  bool is_ready_;
  
  bool is_shutdown_;
  std::string version_override_;
  std::string name_override_;
  int badge_count_ = 0;
#if defined(OS_MACOSX)
  base::DictionaryValue about_panel_options_;
#endif
  DISALLOW_COPY_AND_ASSIGN(Browser);
};
}  
#endif