If Ubuntu 9.10 boots up to a flashing screen and unresponsive keyboard chances are your xwindows configuration isn't working - you can check this by running /etc/init.d/gdm stop (you should have a nice non-flashing shell)
for some reason dpkg-reconfigure xserver-xorg didn't work for but simply deleting /etc/X11/xorg.conf did - all should be fine after a reboot