I believe they are not appearing because you have commented out the rsync block in 45xsession. As you are probably aware, the rsync block copies /etc/skel to /home/user (normally knoppix) on boot up. Contained in /etc/skel are some KDE configuration settings that are not being synced as well.

What is your requirement for a permanent home directory? Or do you mean persistent home directory of which there are cheat codes available for?