Ok, an update: I've got Ubuntu working again (it died on me a while ago). What's interesting though is that that when I start a Unity session NWN runs all clunky, but when I logout and select to login with Gnome the game runs fine.
Oh I'm quite a linux noob, but trying to learn
'>
My startup script is now:
#!/bin/sh
# This script runs Neverwinter Nights from the current directory
export SDL_MOUSE_RELATIVE=0
export SDL_VIDEO_X11_DGAMOUSE=0
# If you do not wish to use the SDL library included in the package, remove
# ./lib from LD_LIBRARY_PATH
# export LD_LIBRARY_PATH=./lib:./miles:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=:./miles:$LD_LIBRARY_PATH
./nwmain $@