Thanks to all:
Try also setting in /etc/kde3/kdm/kdmrc AllowRootLogin=false to true.
Did that and while root doesn't show up on the user list, I can log in by typing root and the password and get an x session going.

I believe this happened when updating kdesktop in a console (alt-f2) session. I have had kdm issues before and will sometimes remove (with --purge) kdm, install xdm or gdm etc.

I wonder if losing the root login was a result of installing in a non gui shell. Anyway thanks again everybody.