There is something missing when bootmisc.sh is running. I believed it has something to do with this line:
echo "System bootup in progress - please wait" > /etc/nologin
cp /etc/nologin /etc/nologin.boot

Check if rmnologin script is also running.
update-rc.d rmnologin defaults


If you run knoppix with Desktop.......it will boot to level5 (init5).
So the prefered location will be /etc/rc5.d.
But if you want to run that script on all level you, put it in rcS.d.
It will be just fine if you just run : update-rc.d <nameofscript> default......and let the script handle it.