I'm having the same issue. My steps are:

  1. tar xfjp stage3-x86-2006.1.tar.bz2 -C stage
  2. tar xfjp portage-20070304.tar.bz2 -C stage/usr
  3. linux32 chroot stage /bin/bash --login
  4. env-update
  5. emerge -u system

Emerge craps out on GCC with the following:
<pre>
{ ./nm -pg libgcc/./_muldi3_s.o libgcc/./_negdi2_s.o libgcc/./_lshrdi3_s.o libgcc/./_ashldi3_s.o libgcc/./_ashrdi3_s.o libgcc/./_cmpdi2_s.o libgcc/./_ucmpdi2_s.o libgcc/./_floatdidf_s.o libgcc/./_floatdisf_s.o libgcc/./_fixunsdfsi_s.o libgcc/./_fixunssfsi_s.o libgcc/./_fixunsdfdi_s.o libgcc/./_fixdfdi_s.o libgcc/./_fixunssfdi_s.o libgcc/./_fixsfdi_s.o libgcc/./_fixxfdi_s.o libgcc/./_fixunsxfdi_s.o libgcc/./_floatdixf_s.o libgcc/./_fixunsxfsi_s.o libgcc/./_fixtfdi_s.o libgcc/./_fixunstfdi_s.o libgcc/./_floatditf_s.o libgcc/./_clear_cache_s.o libgcc/./_enable_execute_stack_s.o libgcc/./_trampoline_s.o libgcc/./__main_s.o libgcc/./_absvsi2_s.o libgcc/./_absvdi2_s.o libgcc/./_addvsi3_s.o libgcc/./_addvdi3_s.o libgcc/./_subvsi3_s.o libgcc/./_subvdi3_s.o libgcc/./_mulvsi3_s.o libgcc/./_mulvdi3_s.o libgcc/./_negvsi2_s.o libgcc/./_negvdi2_s.o libgcc/./_ctors_s.o libgcc/./_ffssi2_s.o libgcc/./_ffsdi2_s.o libgcc/./_clz_s.o libgcc/./_clzsi2_s.o libgcc/./_clzdi2_s.o libgcc/./_ctzsi2_s.o libgcc/./_ctzdi2_s.o libgcc/./_popcount_tab_s.o libgcc/./_popcountsi2_s.o libgcc/./_popcountdi2_s.o libgcc/./_paritysi2_s.o libgcc/./_paritydi2_s.o libgcc/./_powisf2_s.o libgcc/./_powidf2_s.o libgcc/./_powixf2_s.o libgcc/./_powitf2_s.o libgcc/./_mulsc3_s.o libgcc/./_muldc3_s.o libgcc/./_mulxc3_s.o libgcc/./_multc3_s.o libgcc/./_divsc3_s.o libgcc/./_divdc3_s.o libgcc/./_divxc3_s.o libgcc/./_divtc3_s.o libgcc/./_divdi3_s.o libgcc/./_moddi3_s.o libgcc/./_udivdi3_s.o libgcc/./_umoddi3_s.o libgcc/./_udiv_w_sdiv_s.o libgcc/./_udivmoddi4_s.o libgcc/./unwind-dw2_s.o libgcc/./unwind-dw2-fde-glibc_s.o libgcc/./unwind-sjlj_s.o libgcc/./gthr-gnat_s.o libgcc/./unwind-c_s.o; echo %%; \
  cat /var/tmp/portage/gcc-4.1.1-r3/work/gcc-4.1.1/gcc/libgcc-std.ver /var/tmp/portage/gcc-4.1.1-r3/work/gcc-4.1.1/gcc/config/libgcc-glibc.ver \
    | sed -e '/^[   ]*#/d' \
          -e 's/^%\(if\|else\|elif\|endif\|define\)/#\1/' \
    |  ./xgcc -B./ -B/usr/i386-pc-linux-gnu/bin/ -isystem /usr/i386-pc-linux-gnu/include -isystem /usr/i386-pc-linux-gnu/sys-include -L/var/tmp/portage/gcc-4.1.1-r3/work/build/gcc/../ld -O2  -O2 -O2 -mtune=i686 -pipe  -DIN_GCC    -W -Wall -Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes -Wold-style-definition  -isystem ./include  -fPIC -g -DHAVE_GTHR_DEFAULT -DIN_LIBGCC2 -D__GCC_FLOAT_NOT_NEEDED  -I. -I. -I/var/tmp/portage/gcc-4.1.1-r3/work/gcc-4.1.1/gcc -I/var/tmp/portage/gcc-4.1.1-r3/work/gcc-4.1.1/gcc/. -I/var/tmp/portage/gcc-4.1.1-r3/work/gcc-4.1.1/gcc/../include -I/var/tmp/portage/gcc-4.1.1-r3/work/gcc-4.1.1/gcc/../libcpp/include   -E -xassembler-with-cpp -; \
} | gawk -f /var/tmp/portage/gcc-4.1.1-r3/work/gcc-4.1.1/gcc/mkmap-symver.awk  > libgcc/./tmp-libgcc.map
cc1: error: stdout: Value too large for defined data type
mv 'libgcc/./tmp-libgcc.map' libgcc/./libgcc.map
./xgcc -B./ -B/usr/i386-pc-linux-gnu/bin/ -isystem /usr/i386-pc-linux-gnu/include -isystem /usr/i386-pc-linux-gnu/sys-include -L/var/tmp/portage/gcc-4.1.1-r3/work/build/gcc/../ld -O2  -O2 -O2 -mtune=i686 -pipe  -DIN_GCC    -W -Wall -Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes -Wold-style-definition  -isystem ./include  -fPIC -g -DHAVE_GTHR_DEFAULT -DIN_LIBGCC2 -D__GCC_FLOAT_NOT_NEEDED  -shared -nodefaultlibs -Wl,--soname=libgcc_s.so.1 -Wl,--version-script=libgcc/./libgcc.map -o ./libgcc_s.so.1.tmp  libgcc/./_muldi3_s.o libgcc/./_negdi2_s.o libgcc/./_lshrdi3_s.o libgcc/./_ashldi3_s.o libgcc/./_ashrdi3_s.o libgcc/./_cmpdi2_s.o libgcc/./_ucmpdi2_s.o libgcc/./_floatdidf_s.o libgcc/./_floatdisf_s.o libgcc/./_fixunsdfsi_s.o libgcc/./_fixunssfsi_s.o libgcc/./_fixunsdfdi_s.o libgcc/./_fixdfdi_s.o libgcc/./_fixunssfdi_s.o libgcc/./_fixsfdi_s.o libgcc/./_fixxfdi_s.o libgcc/./_fixunsxfdi_s.o libgcc/./_floatdixf_s.o libgcc/./_fixunsxfsi_s.o libgcc/./_fixtfdi_s.o libgcc/./_fixunstfdi_s.o libgcc/./_floatditf_s.o libgcc/./_clear_cache_s.o libgcc/./_enable_execute_stack_s.o libgcc/./_trampoline_s.o libgcc/./__main_s.o libgcc/./_absvsi2_s.o libgcc/./_absvdi2_s.o libgcc/./_addvsi3_s.o libgcc/./_addvdi3_s.o libgcc/./_subvsi3_s.o libgcc/./_subvdi3_s.o libgcc/./_mulvsi3_s.o libgcc/./_mulvdi3_s.o libgcc/./_negvsi2_s.o libgcc/./_negvdi2_s.o libgcc/./_ctors_s.o libgcc/./_ffssi2_s.o libgcc/./_ffsdi2_s.o libgcc/./_clz_s.o libgcc/./_clzsi2_s.o libgcc/./_clzdi2_s.o libgcc/./_ctzsi2_s.o libgcc/./_ctzdi2_s.o libgcc/./_popcount_tab_s.o libgcc/./_popcountsi2_s.o libgcc/./_popcountdi2_s.o libgcc/./_paritysi2_s.o libgcc/./_paritydi2_s.o libgcc/./_powisf2_s.o libgcc/./_powidf2_s.o libgcc/./_powixf2_s.o libgcc/./_powitf2_s.o libgcc/./_mulsc3_s.o libgcc/./_muldc3_s.o libgcc/./_mulxc3_s.o libgcc/./_multc3_s.o libgcc/./_divsc3_s.o libgcc/./_divdc3_s.o libgcc/./_divxc3_s.o libgcc/./_divtc3_s.o libgcc/./_divdi3_s.o libgcc/./_moddi3_s.o libgcc/./_udivdi3_s.o libgcc/./_umoddi3_s.o libgcc/./_udiv_w_sdiv_s.o libgcc/./_udivmoddi4_s.o libgcc/./unwind-dw2_s.o libgcc/./unwind-dw2-fde-glibc_s.o libgcc/./unwind-sjlj_s.o libgcc/./gthr-gnat_s.o libgcc/./unwind-c_s.o -lc && rm -f ./libgcc_s.so && if [ -f ./libgcc_s.so.1 ]; then mv -f ./libgcc_s.so.1 ./libgcc_s.so.1.backup; else true; fi && mv ./libgcc_s.so.1.tmp ./libgcc_s.so.1 && ln -s libgcc_s.so.1 ./libgcc_s.so
/usr/i386-pc-linux-gnu/bin/ld:libgcc/./libgcc.map:1: syntax error in VERSION script
collect2: ld returned 1 exit status
make[3]: *** [libgcc_s.so] Error 1
make[3]: Leaving directory `/var/tmp/portage/gcc-4.1.1-r3/work/build/gcc'
make[2]: *** [libgcc.a] Error 2
make[2]: Leaving directory `/var/tmp/portage/gcc-4.1.1-r3/work/build/gcc'
make[1]: *** [stage1_build] Error 2
make[1]: Leaving directory `/var/tmp/portage/gcc-4.1.1-r3/work/build/gcc'
make: *** [profiledbootstrap] Error 2

!!! ERROR: sys-devel/gcc-4.1.1-r3 failed.
Call stack:
  ebuild.sh, line 1539:   Called dyn_compile
  ebuild.sh, line 939:   Called src_compile
  ebuild.sh, line 1248:   Called toolchain_src_compile
  toolchain.eclass, line 26:   Called gcc_src_compile
  toolchain.eclass, line 1550:   Called gcc_do_make
  toolchain.eclass, line 1424:   Called die

!!! emake failed with profiledbootstrap
!!! If you need support, post the topmost build error, and the call stack if relevant.
</pre>

My emerge --info is:
<pre>
Portage 2.1-r2 (default-linux/x86/no-nptl, gcc-4.1.1, glibc-2.3.6-r4, 2.6.18-smp i686)
=================================================================
System uname: 2.6.18-smp i686 Intel(R) Core(TM)2 CPU          6300  @ 1.86GHz
Gentoo Base System version 1.12.1
app-admin/eselect-compiler: [Not Present]
dev-java/java-config: 2.0.31
dev-lang/python:     2.4.3-r1
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache:     [Not Present]
dev-util/confcache:  [Not Present]
sys-apps/sandbox:    1.2.17
sys-devel/autoconf:  2.13, 2.61
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10
sys-devel/binutils:  2.16.1-r3
sys-devel/gcc-config: 1.3.14
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.17-r2
ACCEPT_KEYWORDS="x86"
AUTOCLEAN="yes"
CBUILD="i386-pc-linux-gnu"
CFLAGS="-O2 -mtune=i686 -pipe"
CHOST="i386-pc-linux-gnu"
CONFIG_PROTECT="/etc"
CONFIG_PROTECT_MASK="/etc/env.d /etc/gconf /etc/terminfo"
CXXFLAGS="-O2 -mtune=i686 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig ccache confcache distlocks metadata-transfer parallel-fetch sandbox sfperms strict"
GENTOO_MIRRORS="http://gentoo.mirrors.tds.net/gentoo/"
LANG="en_US.UTF-8"
MAKEOPTS="-j4"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude='/distfiles' --exclude='/local' --exclude='/packages'"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="x86 alsa apache2 apm arts berkdb bitmap-fonts cli cracklib crypt dri eds emboss encode foomaticdb fortran gdbm gif gnome gpm gstreamer gtk gtk2 iconv imlib ipv6 isdnlog java jpeg kde libg++ libwww mad midi mikmod minimal motif mp3 mpeg ncurses nls ogg opengl oss pam pcre perl png pppd python qt3 qt4 quicktime readline reflection ruby session spell spl ssl tcpd threads truetype truetype-fonts type1-fonts vorbis xml xorg xv zlib alsa_cards_ali5451 alsa_cards_als4000 alsa_cards_atiixp alsa_cards_atiixp-modem alsa_cards_bt87x alsa_cards_ca0106 alsa_cards_cmipci alsa_cards_emu10k1 alsa_cards_emu10k1x alsa_cards_ens1370 alsa_cards_ens1371 alsa_cards_es1938 alsa_cards_es1968 alsa_cards_fm801 alsa_cards_hda-intel alsa_cards_intel8x0 alsa_cards_intel8x0m alsa_cards_maestro3 alsa_cards_trident alsa_cards_usb-audio alsa_cards_via82xx alsa_cards_via82xx-modem alsa_cards_ymfpci alsa_pcm_plugins_adpcm alsa_pcm_plugins_alaw alsa_pcm_plugins_asym alsa_pcm_plugins_copy alsa_pcm_plugins_dmix alsa_pcm_plugins_dshare alsa_pcm_plugins_dsnoop alsa_pcm_plugins_empty alsa_pcm_plugins_extplug alsa_pcm_plugins_file alsa_pcm_plugins_hooks alsa_pcm_plugins_iec958 alsa_pcm_plugins_ioplug alsa_pcm_plugins_ladspa alsa_pcm_plugins_lfloat alsa_pcm_plugins_linear alsa_pcm_plugins_meter alsa_pcm_plugins_mulaw alsa_pcm_plugins_multi alsa_pcm_plugins_null alsa_pcm_plugins_plug alsa_pcm_plugins_rate alsa_pcm_plugins_route alsa_pcm_plugins_share alsa_pcm_plugins_shm alsa_pcm_plugins_softvol elibc_glibc input_devices_keyboard input_devices_mouse input_devices_evdev kernel_linux lcd_devices_bayrad lcd_devices_cfontz lcd_devices_cfontz633 lcd_devices_glk lcd_devices_hd44780 lcd_devices_lb216 lcd_devices_lcdm001 lcd_devices_mtxorb lcd_devices_ncurses lcd_devices_text userland_GNU video_cards_apm video_cards_ark video_cards_ati video_cards_chips video_cards_cirrus video_cards_cyrix video_cards_dummy video_cards_fbdev video_cards_glint video_cards_i128 video_cards_i740 video_cards_i810 video_cards_imstt video_cards_mga video_cards_neomagic video_cards_nsc video_cards_nv video_cards_rendition video_cards_s3 video_cards_s3virge video_cards_savage video_cards_siliconmotion video_cards_sis video_cards_sisusb video_cards_tdfx video_cards_tga video_cards_trident video_cards_tseng video_cards_v4l video_cards_vesa video_cards_vga video_cards_via video_cards_vmware video_cards_voodoo"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, LDFLAGS, LINGUAS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY
</pre>

I was poking around in /var/tmp/portage/gcc-4.1.1-r3/work/build and tried running:

<pre>
{ ./nm -pg libgcc/./_muldi3_s.o libgcc/./_negdi2_s.o libgcc/./_lshrdi3_s.o libgcc/./_ashldi3_s.o libgcc/./_ashrdi3_s.o libgcc/./_cmpdi2_s.o libgcc/./_ucmpdi2_s.o libgcc/./_floatdidf_s.o libgcc/./_floatdisf_s.o libgcc/./_fixunsdfsi_s.o libgcc/./_fixunssfsi_s.o libgcc/./_fixunsdfdi_s.o libgcc/./_fixdfdi_s.o libgcc/./_fixunssfdi_s.o libgcc/./_fixsfdi_s.o libgcc/./_fixxfdi_s.o libgcc/./_fixunsxfdi_s.o libgcc/./_floatdixf_s.o libgcc/./_fixunsxfsi_s.o libgcc/./_fixtfdi_s.o libgcc/./_fixunstfdi_s.o libgcc/./_floatditf_s.o libgcc/./_clear_cache_s.o libgcc/./_enable_execute_stack_s.o libgcc/./_trampoline_s.o libgcc/./__main_s.o libgcc/./_absvsi2_s.o libgcc/./_absvdi2_s.o libgcc/./_addvsi3_s.o libgcc/./_addvdi3_s.o libgcc/./_subvsi3_s.o libgcc/./_subvdi3_s.o libgcc/./_mulvsi3_s.o libgcc/./_mulvdi3_s.o libgcc/./_negvsi2_s.o libgcc/./_negvdi2_s.o libgcc/./_ctors_s.o libgcc/./_ffssi2_s.o libgcc/./_ffsdi2_s.o libgcc/./_clz_s.o libgcc/./_clzsi2_s.o libgcc/./_clzdi2_s.o libgcc/./_ctzsi2_s.o libgcc/./_ctzdi2_s.o libgcc/./_popcount_tab_s.o libgcc/./_popcountsi2_s.o libgcc/./_popcountdi2_s.o libgcc/./_paritysi2_s.o libgcc/./_paritydi2_s.o libgcc/./_powisf2_s.o libgcc/./_powidf2_s.o libgcc/./_powixf2_s.o libgcc/./_powitf2_s.o libgcc/./_mulsc3_s.o libgcc/./_muldc3_s.o libgcc/./_mulxc3_s.o libgcc/./_multc3_s.o libgcc/./_divsc3_s.o libgcc/./_divdc3_s.o libgcc/./_divxc3_s.o libgcc/./_divtc3_s.o libgcc/./_divdi3_s.o libgcc/./_moddi3_s.o libgcc/./_udivdi3_s.o libgcc/./_umoddi3_s.o libgcc/./_udiv_w_sdiv_s.o libgcc/./_udivmoddi4_s.o libgcc/./unwind-dw2_s.o libgcc/./unwind-dw2-fde-glibc_s.o libgcc/./unwind-sjlj_s.o libgcc/./gthr-gnat_s.o libgcc/./unwind-c_s.o; echo %%;   cat /var/tmp/portage/gcc-4.1.1-r3/work/gcc-4.1.1/gcc/libgcc-std.ver /var/tmp/portage/gcc-4.1.1-r3/work/gcc-4.1.1/gcc/config/libgcc-glibc.ver     | sed -e '/^[   ]*#/d'           -e 's/^%\(if\|else\|elif\|endif\|define\)/#\1/'     |  ./xgcc -B./ -B/usr/i386-pc-linux-gnu/bin/ -isystem /usr/i386-pc-linux-gnu/include -isystem /usr/i386-pc-linux-gnu/sys-include -L/var/tmp/portage/gcc-4.1.1-r3/work/build/gcc/../ld -O2  -O2 -O2 -mtune=i686 -pipe  -DIN_GCC    -W -Wall -Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes -Wold-style-definition  -isystem ./include  -fPIC -g -DHAVE_GTHR_DEFAULT -DIN_LIBGCC2 -D__GCC_FLOAT_NOT_NEEDED  -I. -I. -I/var/tmp/portage/gcc-4.1.1-r3/work/gcc-4.1.1/gcc -I/var/tmp/portage/gcc-4.1.1-r3/work/gcc-4.1.1/gcc/. -I/var/tmp/portage/gcc-4.1.1-r3/work/gcc-4.1.1/gcc/../include -I/var/tmp/portage/gcc-4.1.1-r3/work/gcc-4.1.1/gcc/../libcpp/include   -E -xassembler-with-cpp -; } | gawk -f /var/tmp/portage/gcc-4.1.1-r3/work/gcc-4.1.1/gcc/mkmap-symver.awk
</pre>

by hand, but I would end up getting a "cc1: error: stdout: Value too large for defined data type" error.