Well, Ubuntu is still finding ways to upset the apple cart. Had a usual upgrade window come up, so pressed OK, but it also included a kernel version upgrade, and once again, I ended up with a system that wont boot. Eventually I had to boot from a LiveCD, edit the /etc/X11/xorg.conf file and change "nvidia" to "vesa". Once back in to Ubuntu, I cleaned out a lot of rubbish from said file, and then reinstalled the nvidia drivers.
There does appear to be an issue with my system not recompiling the nvidia stuff for any new kernels that get installed, yet other people seem to be OK.
Although this was on Koala, I did have the problem with the previous version Jaunty as well, so its probably time to reinstall the OS from scratch to get back to some sensible setting. Possible that cleaning out xorg.conf may have helped though.