In Gentoo, by default the xorg server is now built in a way that it relies on hal, a typical case of premature release, features working out of the box were sacrificed for some unneeded or even unwanted flexibility. You are supposed to edit some so-called fdi files for hal, but whenever somebody tells you that you should fiddle around with XML files because it would make your life easier or better, don't believe them. It's a lie, always.

The effect of this premature change is that settings for input devices like mouse, keyboard and so in in your /etc/X11/xorg.conf are ignored, and you suddenly end up with a US keyboard layout (although you configured another one), or a mouse without scroll wheel.

If you can't help going the hard way, follow the Gentoo Xorg 1.5 Upgrade Guide. Otherwise, just disable the hal support in Xorg until it is really working:

# echo "x11-base/xorg-server -hal" >>/etc/portage/package.use
# emerge --update --newuses xorg-server