I don't have time to go into all the feedback now (need sleep ... zzz), but it looks like a false positive. I'll expect a few of those once in a while. The machine is my home machine, so I'm usually pounding on the keys when chkrootkit runs. Ho hum.
I'll probably reinstall in a few weeks time (Gnome2 being due, and time getting more available) and change passwords, GPG keys, etc. Trouble is there's always something else as well... Thanks for the feedback. I have some thinking to do. One more episode in the tale of a paranoid security newbie :/