No, it's not kpsewhich, it's probably your debconf answers. As a
temporary solution, run dpkg-reconfigure tetex-bin, and choose to manage
fmtutil.cnf and updmap.cfg through debconf. Also, you should make sure
that the commands
egrep '^VARTEXMF|^TEXMF ' /etc/texmf/texmf.cnf
egrep '^VARTEXMF|^TEXMF ' /etc/texmf/texmf.d/05TeXMF.cnf
give the same output, namely
VARTEXMF = /var/lib/texmf
TEXMF = {$HOMETEXMF,!!$TEXMFLOCAL,!!$TEXMFOLDLOCAL,!!$VARTEXMF,!!$TEXMFMAIN}
If update-texmf does not achieve this, this means you have edited
/etc/texmf/texmf.cnf manually, and when ucf asked you upon upgrade, you
refused to accept the maintainers' changes. You need those two lines in
/etc/texmf/texmf.cnf - either edit it manually again, or you can:
# mv /etc/texmf/texmf.cnf texmf.cnf-save.copy
# ucf --purge /etc/texmf/texmf.cnf
# update-texmf
(now check again with egrep '^VARTEXMF|^TEXMF ' /etc/texmf/texmf.cnf)
and optionally
# diff texmf.cnf-save.copy /etc/texmf/texmf.cnf
# $EDITOR /etc/texmf/texmf.cnf
and make your changes again.
P.S I have marked this bug as grave, because it makes latex unusable on
my system. If this is in fact NOT a problem for everybody, then please
forgive my exxageration.
It's probably a problem for everybody who is not reading the diff's that
dpkg and ucf offer when a conffile is updated.
Regards, Frank