well if your computer is networked you can shoot the files over to it to back up then do a format. YOu could ether use a windows spc (needs to be shareing a folder) or another linux computer. (you can run knoppix again if you wish, ether get another disk or use the terminal server (see forum for more details)

If you have another hardrive you can just pop that in a back up to it.

As for finding out what is wrong with windows I can't help.