Hi Daniel,
and the 'active' one (according to kpsewhich and texmf.cnf) is
/usr/local/texlive/2008/texmf-config/web2c/updmap.cfg
The question seems to be, where did the one in texmf-config come from?
Any idea?
updmap and tlmgr write to texmf-var, as far as I could tell. When I
do a fresh test install, it's also in texmf-var ...