ok heres the just of it the new phpconfig / php separation seems to have broken all module installations; phpconfig does not pick up the config settings that your php install is using and then will build modules incorrectly more specifically apc / eaccelerator will build with debug on when it should be off and the module will then fail to load; i have simply fixed this by removing the "rm -f"'s from the eclass which is basically just removing the need for phpconfig this should be addressed soon.
We'll probably remove phpconfig; it hasn't worked out as well as it has for Debian. Please keep an eye on http://planet.gentoo.org/ for news about work on php5 support in Gentoo. Best regards, Stu