I did some more playing around with this and I found my GDMSESSION
variable is set to "default". If I add:

export GDMSESSION="$DESKTOP_SESSION"

if [ "$GDMSESSION" = "default" ] ; then
        export GDMSESSION=gnome
fi

then Unity will start correctly. It doesn't seem to cause any problems if the 
session type is changed prior to login either. 
I'm not sure why just 'export GDMSESSION="$DESKTOP_SESSION"' doesn't work for 
me, but I've tested this over several 11.04 x86_64 installs now using a clean 
(no data/config in the $HOME directory) account.

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https://bugs.launchpad.net/bugs/772486

Title:
  [Natty] Unity will start from GDM, not from KDM

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