I followed the path of calling ApplyConfiguration from a script upon
docking, and while it is not pretty, it basically works:

# cat /etc/udev/rules.d/80-thinkpad-T61.rules 
KERNEL=="dock.0", ATTR{docked}=="1", RUN+="/usr/local/bin/dock.sh 1"
KERNEL=="dock.0", ATTR{docked}=="0", RUN+="/usr/local/bin/dock.sh 0"

# cat /usr/local/bin/dock.sh 
#!/bin/sh

LOG=/tmp/dock.$$

echo "Called dock.sh with $@, proceeding" > ${LOG}

if [ $1 -eq 1 ]; then
  DISPLAY=:0.0
  export DISPLAY
  sudo -u ubuntu dbus-send --type="method_call" --print-reply --session 
--dest=org.gnome.SettingsDaemon /org/gnome/SettingsDaemon/XRANDR 
org.gnome.SettingsDaemon.XRANDR.ApplyConfiguration 2>&1 >> ${LOG}
fi

echo "Done docking" >> ${LOG}


Is this path worth pursuing or is this approach out of question for fixing the 
problem?

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https://bugs.launchpad.net/bugs/732867

Title:
  gnome-display-properties monitor layout not saved when re-docking (and
  display port)

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