As of today, dev-lang/php-5.{3.25,4.15,5.0_rc1}.ebuild dev-lang/PEAR-PEAR-1.9.{3,4}.ebuild still refer to /etc/make.conf instead of /etc/portage/make.conf when emerged
This may be a duplicate of bug 467648 (which is marked as fixed but I think it isn't).
fixed in both dev-lang/php and dev-php/PEAR-PEAR