My Gentoo updated xinit and X to 1.2.0-r3 and 1.6.5 (I am not sure if the change were made in them, the changes should be made around after 2009-12-08), then XDM didn't bring up fluxbox but the twm.

Here is a related post on Gentoo Forums. In simple words, XSESSION in rc.conf won't be working anymore. You have to do this, in case of fluxbox, as root:
echo "XSESSION=fluxbox" > /etc/env.d/90xsession
env-update

Once you click on shutdown in xsm and login again, it should be working.

PS. I have to reboot, one of my monitors didn't work after turning on using xrandr but fluxbox does.