So, I'm not familiar with Nux, the GUI toolkit that Unity uses.
unity/src/PanelTray.cpp has these tantalizing lines of code:

    void
    PanelTray::Draw (nux::GraphicsEngine& gfx_content, bool force_draw)
    {
      nux::Geometry geo = GetGeometry ();

      if (geo.x != _last_x || geo.y != _last_y)
      {
        _last_x = geo.x;
        _last_y = geo.y;

        gtk_window_move (GTK_WINDOW (_window), geo.x + PADDING, geo.y);
      }
    }

It appears to me that geo contains coordinates relative to the parent
widget (which is the panel), while _window is a top-level window and
wants absolute screen coordinates, and therefore this works only when
the panel is at +0+0.  If only I knew how to convert relative
coordinates to absolute ones in Nux...

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https://bugs.launchpad.net/bugs/778256

Title:
  Notification area ("system tray") missing when using dual monitors of
  different sizes, with their bottoms aligned

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