CONFIG_PROTECT_MASK via emerge --info: CONFIG_PROTECT_MASK="${EPREFIX}/etc/gconf /etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" should be CONFIG_PROTECT_MASK="/etc/gconf /etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" This is on a system running without prefix.
Try re-syncing and re-emerging gconf
Timestamp of tree: Fri, 10 May 2013 09:00:01 +0000 as far as I can see, it is fixed in gconf-3.2.6, but not in gconf-2.32.4
+*gconf-2.32.4-r1 (10 May 2013) + + 10 May 2013; Gilles Dartiguelongue <eva@gentoo.org> +gconf-2.32.4-r1.ebuild: + Stable bump: apply prefix fixes to stable ebuild, bug #469240. + Looks like the fix didn't make it to stable. This is now fixed, thanks for reporting.