This may be related to bug #47387, but the solution provided (re-emerge baselayout and module-init-tools) didn't help. The problem appears to be caused by the generate-modprobe.conf script failing to find an old version of modprobe i.e. one whose version string contains "modprobe version" instead of "module-init-tools version". The script also tries to find modprobe.old - I don't have one. With module-init-tools 3.1, running "modprobe -c" appears to generate valid output provided that everything below and including the comment "Aliases extracted from modules themselves." is removed. I imagine this could be done in the script using sed? Reproducible: Always Steps to Reproduce: Actual Results: # modules-update * Warning: could not generate /etc/modprobe.conf! # generate-modprobe.conf Cannot find old version of modprobe. Giving up. Portage 2.0.51-r3 (default-linux/amd64/2004.3, gcc-3.4.3, glibc-2.3.4.20041102-r0, 2.6.9-gentoo-r6 x86_64) ================================================================= System uname: 2.6.9-gentoo-r6 x86_64 AMD Athlon(tm) 64 Processor 3500+ Gentoo Base System version 1.6.6 Autoconf: sys-devel/autoconf-2.59-r5 Automake: sys-devel/automake-1.8.5-r1 Binutils: sys-devel/binutils-2.15.92.0.2-r1 Headers: sys-kernel/linux26-headers-2.6.8.1-r1 Libtools: sys-devel/libtool-1.5.2-r7 ACCEPT_KEYWORDS="amd64 ~amd64" AUTOCLEAN="yes" CFLAGS="-march=athlon64 -O3 -pipe" CHOST="x86_64-pc-linux-gnu" COMPILER="" CONFIG_PROTECT="/etc /usr/X11R6/lib/X11/xkb /usr/kde/2/share/config /usr/kde/3.3/env /usr/kde/3.3/share/config /usr/kde/3.3/shutdown /usr/kde/3/share/config /usr/share/config /var/qmail/control" CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/env.d" CXXFLAGS="-march=athlon64 -O3 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="autoaddcvs autoconfig ccache distlocks sandbox" GENTOO_MIRRORS="ftp://mirror.pacific.net.au/linux/Gentoo ftp://mirror.isp.net.au/pub/gentoo/ ftp://planetmirror.com/pub/gentoo/" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="" SYNC="rsync://rsync.au.gentoo.org/gentoo-portage" USE="amd64 X Xaw3d aalib acpi adns alsa apache2 arts audiofile authdaemond avi berkdb bitmap-fonts cddb cdparanoia cdr chroot crypt cscope cups curl divx4linuxdjbfft dmx dv dvd dvdr encode esd f77 faac faad fam fbcon flac foomaticdb fortran fpx freetype gdbm gif gimpprint gpm gps graphviz gtk gtk2 imagemagick imap imlib jack java jbig jp2 jpeg jpeg2k junit kde lcms libcaca lm_sensors lzw lzw-tiff mad maildir mikmod mmap mng motif mozdevelop mpeg multilib ncurses nls no-old-linux nptl nvidia offensive oggvorbis openal opengl pam pda perl png povray ppdspython qt quicktime readline sdk sdl slang sndfile snmp spamassassin speex spell ssl svg tcltk tcpd theora tiff truetype usb userlocales virus-scan wmf xine xml xml2 xmms xpm xprint xrandr xscreensaver xv yv12 zlib"
Problem was caused by having the "no-old-linux" USE flag set.
If you have not seen: Bug #66504 is about this problem too.