The files in backup will override those in /etc/skel/ (for good reason). The new files don't contain your settings, like for jwm_keys, and don't necessarily work. /etc/skel/.xsession results in a big "X", probably because the tests don't work correctly on my setup for some reason.
edit: /etc/skel/.xsession needs "DESKTOP=`/etc/sysconfig/desk`" On my copy, it also works better if I use if/thens.