I think you also need to do:

Code:
cp -ar /mnt-system/boot /mnt/hda1/knx/master/boot
If you want to autorun scripts with LXDE, you have to

create /etc/xdg/autostart/someentry.desktop containing:
Code:
[Desktop Entry]
Name=Somename
Comment=Scanner
Type=Application
Exec=/home/knoppix/somescript.py
Terminal=false
X-GNOME-Autostart-enabled=true
I also wanted to run a root mount script, which I did by creating another file in the same dir of somerootscript.desktop
Code:
[Desktop Entry]
Name=somerootscript
Comment=Somescript
Type=Application
Exec=/home/knoppix/rootscript.sh
Terminal=false
X-GNOME-Autostart-enabled=true
in /home/knoppix/rootscript.sh I put
Code:
#!/bin/bash
sudo /pathtorootscript/rootscript.sh
and that all worked. This took a ton of time to figure out, I hope it helps.