After I recompiled X (x11-base/xorg-x11-6.8.2-r6) etc-update complained about updated config files that were actually recompiled binaries, like /usr/lib/X11/xkb/xkbcomp and a few others. I'm not completely sure how conffile flagging works in Gentoo, but these files should probably be unflagged somehow :-)
*** This bug has been marked as a duplicate of 17268 ***