I'm currently playing again with Gentoo and I'm getting again the “One of the files in /etc/{conf.d,init.d} or /etc/rc.conf has a modification time in the future”-error. So here is some help, if you have the same little annoyance.
Here it was the case, that the file in /etc/conf.d and /etc/init.d had no timestamp (you can check with ls -lR). You can solve this by a hearty
touch /etc/{conf.d,init.d}/* /etc/rc.conf[ Solution found at forums.gentoo.org ]