sadly, knoppix isnt fully debian compattible. I recommend using kanotix or mephis for hdinstall. yo can quickly get on track again by saving your /etc and replacing the modifications you.ve made after re-install. and your home can even simply be copied (think about the user rights!!!).

and your current packages selection (guess you've installed and removed packages...) can be restored using this:
"dpkg --get-selections > selections.txt"
copies a list of the status of you'r software to selections.txt

on your new system:
"dpkg --set-selections < selections.txt"
tells dpkg this has to be the set of installed software.
then tell apt to apply it:
"apt-get dselect-upgrade"

very easy and fast... I hope this can be made gui asap