As noted in bug #200060, some of the keycodes (special keys like Windows key, arrows, PgUp/PgDown, some numberpad keys) change when switching from xf86 keyboard to an evdev/hal managed one, which seems to happen for nearly everyone with the latest stable hal release. There's nothing gentoo can do about it, but it should warn about these changes when emerging the hal ebuild.
Steps to Reproduce:
1. Emerge >=sys-apps/hal-0.5.10.
2. Don't edit custom-made xmodmaps.
3. Start X
Some modifier keys might not work anymore as expected.
A warning/info should be issued when emerging a newer version of hal.
For a list of differences, look at the changes with:
diff -yw /usr/share/X11/xkb/keycodes/evdev /usr/share/X11/xkb/keycodes/xfree86 | less
Please add your comment to bug 200060 if you feel the need to.
*** This bug has been marked as a duplicate of bug 200060 ***