Thanks hal8000 for the respons!
I will look into your suggestion and maybe also use apt-get from the command line not using the Synaptic gui.

The remastering process I experienced most successful is:
1. Start Knoppix from the original DVD with a "tohd" alternative, then creating a persistent knoppix.img.
2. Making the kde changes and other software upgrades in that environment.
3. Creating incremental knoppix.img backups along the way to get a smooth fallback.
4. When satisfied with the changes I do a "sudo knoppix-installer" in a terminal window with the "knoppix like from CD alternative".
5. That install brings along the changes and upgrades to the Hd-install.
6. Without ever starting the the Hd install I there make the etc/init.d/knoppix-autoconfig changes (language), the /etc/X11/Xsession.d/45xsession changes (add ".config" and delete "{.kde*,Desktop}" and delete the /etc/X11/xorg.conf file.
7. I then rsync (in the Hd install) /home/knoppix/ with /etc/skel.
8. From this Hd install I make the new master using "mkisofs".
9. If the new compressed Knoppix file gets to big (around 4 Gb) it is split into Knoppix and Knoppix2 (using exclude list and graft points). I believe one may also "mv" out the files intended for KNOPPIX2 if using exclude list and graftpoints gets to "messy". In the case of big files I run the new Knoppix from a DL DVD.
10. I have also experienced that "mkisofs" did not like to work from the reiserfs with the Hd install.
11. In that case I simply created a new source from the Hd install as is done when copying files from the original DVD (according to the remastering WIKI).
12 From the new source I then do the compressing with mkisofs.

It was in step 2 I experienced the problem with upgrading software, that is, in the first orignial environment when no remastering efforts were made.
I upgraded about 4 audio applications, Ice Weasel and Ice Ape and added Mozilla mplayer and Flash plugins for Ice Weasel. That went well. I had to back off any upgrades (order in the upgrading sequence was of no significance) that promised to change (cups functionality - printing I believe) lib*.*- files that contained the letter sequence "cups" or else I got stuck with the Knoppix login prompt. Amarok was such an example, Konqueror another.