Well I think there was a problem with the xlibs .deb, as I had the symlink set up correctly - /usr/X11R6/lib/X11/app-defaults was pointing to /etc/X11/app-defaults, but xlibs decided it was wrong and removed it. Then when it tried to update its settings it died due to a broken pipe.
So I mkdir /usr/X11R6/lib/X11/app-defaults and cp -a /etc/X11/app-defaults/* back into it and then re ran the upgrade and it behaved, though told me that there should be a symlink pointing to /etc/X11/app-defaults. Deja-vu? Thanks for you help, and I hope this may be able to help others who come across this one! Matthew -- Using intelligent power: RISC OS, Be OS, Debian Linux Enjoying computing.