One possibility: when you did apt-get dist upgrade, perhaps some of your configs were reset to a default setting. You should still be able to go into control center & change the settings to what you want, although if you're running from CD you will have to use a persistent home to maintain your settings.
Knoppix does load the default settings from /etc/skel when booting from CD, so you have to copy any custom settings from /home/knoppix to /etc/skel before making your remaster f you want to keep them. Also check /etc/X11/xsessiond/45xsession to make sure it is copying everything from /etc/skel. It has a list of the files it copies in the script, you may have to change it to cp /etc/skel/* & /cp/etc/skel.* instaed of the specified list.