Whether this happens or not depends either on the relative position of
the two screens (moving LVDS so that its bottom is lower than the bottom
of VGA seems to trigger this), and on whether I disable the screens with
the gnome-display-settings (no bug), or with 'xrandr --output VGA --auto
--output LVDS --off' (triggers bug).

The exact sequence of commands I can use to reproduce this is

  1. xrandr --output VGA --auto --rotate left --right-of LVDS
  2. xrandr --output LVDS --auto --pos 0x480
  3. xrandr --output LVDS --auto --output VGA --off

-- 
bottom panel jumps to top after turning an external monitor on and off
https://bugs.launchpad.net/bugs/355848
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