I'm not a linux expert, so can someone help me out here?

Building my own remaster, I've installed a couple programs and tested them before building the iso. So far, no harm done.
Then, while testing this iso, I noticed some files were missing and after a while I figured out the cause. I installed and tested all my programs in a chrooted environment and one of the programs uses user specific settings, normally saved in $HOME. While running as root, $HOME ="/" and this causes my problem when starting from CD. As part of the Knoppix startup script, symbolic links are made from /xxx to KNOPPIX/xxx , but not to KNOPPIX/.

Can someone help me out here?
(I could copy this files from /KNOPPIX/ to /, but that doesn't sound neat to me)

Best regards,
Jasper van Dijk