I'm not a knoppix master myself(actually im a newb), but what if you backed up your data then reinstalled? Knoppix i know has CD-burning stuff in it(i used it once, dont remember how exactly tho), you can burn a CD with your data then reinstall. If your logged in as knoppix, you cant write to the /usr directory so you cant install programs until you fix it anyway...

Just a thaught