MAKEOPTS=-j1 emerge -av1 app-emulation/hercules solved this problem for me.
$ emerge --info Portage 2.2.7 (default/linux/x86/13.0, gcc-4.8.1, glibc-2.17, 3.11.3-pf i686) ================================================================= System uname: Linux-3.11.3-pf-i686-Genuine_Intel-R-_CPU_T2080_@_1.73GHz-with-gentoo-2.2 KiB Mem: 1943172 total, 481072 free KiB Swap: 524284 total, 345796 free Timestamp of tree: Tue, 15 Oct 2013 09:30:01 +0000 ld GNU ld (GNU Binutils) 2.23.2 distcc 3.1 i686-pc-linux-gnu [disabled] app-shells/bash: 4.2_p45 dev-java/java-config: 2.2.0 dev-lang/python: 2.7.5-r2, 3.2.5-r2, 3.3.2-r2 dev-util/cmake: 2.8.11.2 dev-util/pkgconfig: 0.28 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.12.2 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.9.6-r3, 1.11.6, 1.13.4, 1.14 sys-devel/binutils: 2.23.2 sys-devel/gcc: 4.8.1-r1 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.11 (virtual/os-headers) sys-libs/glibc: 2.17 Repositories: gentoo crossdev wild-ebuild ACCEPT_KEYWORDS="x86 ~x86" ACCEPT_LICENSE="*" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=prescott -fomit-frame-pointer -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/X11/xinit/xserverrc /etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-O2 -march=prescott -fomit-frame-pointer -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -march=i686 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync metadata-transfer news nodoc noinfo parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -march=i686 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="ru_RU.UTF-8" LC_ALL="" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/portage/local/crossdev /usr/portage/local/wild-ebuild" USE="acl alsa dbus gpm idn midi mmx mmxext nls nptl ocamlopt openmp pam pulseaudio sse sse2 sse3 threads truetype udev unicode x86 xattr xinerama" ABI_X86="32" ALSA_CARDS="hda-intel usb-audio dummy loopback seq-dummy virmidi" CAMERAS="ptp2" ELIBC="glibc" GPSD_PROTOCOLS="aivdm garmin garmintxt gpsclock mtk3301 nmea nmea2000 sirf ubx" GRUB_PLATFORMS="multiboot pc" INPUT_DEVICES="evdev keyboard mouse joystick synaptics" KERNEL="linux" LINGUAS="ru en" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" SANE_BACKENDS="net xerox_mfp" USERLAND="GNU" VIDEO_CARDS="v4l vesa modesetting radeon r300" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON
To reproduce the bug you should first unmerge app-emulation/hercules if you have it installed, otherwise it merges correctly independent of make job number
Created attachment 360948 [details] Build.log
i think it should be fixed now by: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d346d85dce1f865a3f318d645c494e2955f2b239
