After modifying gdm.conf we noticed that Xnewt would not start properly on occassion. Xnewt was not ignoring the vt[0-9] command line option sent to X to specify a virtual console on which to run. We removed this from the command line sent to Xnewt and renamed Xnewt to Xnewt.sun

pushd /usr/X11R6/bin
mv Xnewt Xnewt.sun
echo Xnewt
#!/bin/sh

XFIX=`echo $@ |sed -e's/vt[0-9]*//'`
echo `date`: ARGS=$@ XFIX=$XFIX >>/var/log/Xnewt

exec Xnewt.sun $XFIX -fp unix/:7100
EOF
chmod 755 Xnewt
popd

IBM/Lenovo have a utility to remap the windows key, it's called

TpKmapAp.exe

(Keyboard Customizer Utility) It's in Program Files\ThinkPad\Utilities on our X41's.