See the attached screenshots. I have installed GNOME 2.13 from the official GNOME/SVN overlay on a fresh install of Gentoo Linux (~x86). Portage 2.1_pre4-r1 (default-linux/x86/2005.1, gcc-3.4.5, glibc-2.3.6-r2, 2.6.15-gentoo-r3 i686) ================================================================= System uname: 2.6.15-gentoo-r3 i686 Intel(R) Pentium(R) M processor 1500MHz Gentoo Base System version 1.12.0_pre15 dev-lang/python: 2.4.2-r1 sys-apps/sandbox: 1.2.17 sys-devel/autoconf: 2.13, 2.59-r7 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r1 sys-devel/binutils: 2.16.1-r1 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.6.11-r3 ACCEPT_KEYWORDS="x86 ~x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-march=pentium-m -O2 -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config /usr/share/X11/xkb /usr/share/config /var/qmail/control" CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/texmf/web2c /etc/env.d" CXXFLAGS="-march=pentium-m -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="autoaddcvs autoconfig cvs digest distlocks fixpackages sandbox sfperms sign strict" GENTOO_MIRRORS="ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://trumpetti.atm.tut.fi/gentoo http://gentoo.oregonstate.edu http://www.ibiblio.org/pub/Linux/distributions/gentoo" LINGUAS="de" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/overlay/gnome" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="x86 X a52 aac acpi alsa avi berkdb bitmap-fonts bonjour browserplugin bzip2 cairo cdr crypt cups dbus divx4linux dvd dvdr dvdread eds emboss encode exif fame firefox flac foomaticdb fortran galago gdbm gif glitz gnome gpm gstreamer gtk gtk2 hal howl imlib ipv6 java jpeg libg++ libwww lzo mad matroska mikmod mjpeg mmx mng mono moznocompose moznoirc moznomail mozsvg mp3 mpeg ncurses nls nomotif nptl nsplugin nvidia ogg oggvorbis opengl oss pam pam_console pcre pdflib perl png python quicktime readline spell sse sse2 ssl svg tcpd theora tiff truetype truetype-fonts type1-fonts unicode usb vorbis win32codecs wmf xml2 xv xvid zlib elibc_glibc input_devices_evdev input_devices_keyboard input_devices_mouse input_devices_synaptics kernel_linux linguas_de userland_GNU video_cards_nv video_cards_nvidia" Unset: ASFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, LANG, LC_ALL, LDFLAGS, MAKEOPTS
Created attachment 79087 [details] GNOME 2.13 desktop on first login. The icons are correctly aligned.
Created attachment 79088 [details] GNOME 2.13 desktop after second login. The icons are no longer correctly aligned.
Also reported UPSTREAM at http://bugzilla.gnome.org/show_bug.cgi?id=330298.
Same for 2.14.0
a bit farfetched idea might be that it shows an icon for a short while, but removes it afterwards (not user visible) that pushes the other icons down.
Fixed in nautilus 2.14.1.
Nautilus 2.14.1 is in portage.