I could be wrong but I think it is the script /etc/X11/Xsession.d/45xsession that controls how Knoppix populates the /home/knoppix files. If you check the script, you will see some lines that contain lines that read like:
Code:
rsync -Ha --ignore-existing /etc/skel/{.kde*,Desktop} $HOME/ 2>/dev/null
It is that those logic blocks & rsync commands that populates the /home/knoppix. I am guessing that in your case, the script is using rsync to copy the config files from another location.
I hope this helps.
James