I would have expected the Windows CD to boot regardless of the condition of the hard disk. Maybe your Windows CD is bad?
If you suspect that your CD might be bad, you can try running TestDisk http://www.cgsecurity.org/wiki/TestDisk to see if you can recover your old Windows installation that you just formatted because you can use Knoppix to help you make a new Windows CD from the files on the hard drive by following instructions from http://www.nu2.nu/bootcd/.
You may alternatively be able to use the files from your old CD to make a new CD, but you will need to copy those to a hard drive or USB first unless you have two CD/DVD drives.

To see if the problem is a failing hard disk, first I would open a konsole, and run 'sudo fdisk-lu' ,to find out what drives are detected and what the partition table(s) look like.
Code:
sudo fdisk -lu
If your hard drive comes up as '/dev/sda', then try running the following command on it to get more information about your hard disk, 'sudo smartctl -a /dev/sda >> harddisk.report ',
Code:
sudo smartctl -a /dev/sda >> harddisk.report
Replace '/dev/sda' with '/dev/hda' if applicable, (according to the results from the earlier command).
After you run that command , go and look for a text file named 'harddisk.report' in the knoppix home folder.
Open it and it should show you what kind of hard disk you have, (make and model, and so on), plus lots of other information about your hard disk.
You would need to be an 'ubber geek' to be able to make much sense out of most of the report, but if you look in the part titled 'Vendor Specific SMART Attributes with Thesholds', you should see a column headed 'WHEN FAILED', and if the existence of any entries in that column would be sign that your hard drive has had problems, but it does not mean the hard drive is necessarily bad. Wikipedia has a page about smartmontools that the layman should be able to understand. http://en.wikipedia.org/wiki/Self-Mo...ing_Technology

If you think your hard disk is good, (fdisk 'sees' it, and smartmontools doesn't show up any bad failures), then you might want to erase your entire hard drive with the badblocks command to make sure you get well and truly rid of any viruses, which plague all Windows operating systems.
One way you can do that in Linux, and test your hard disk for bad blocks at the same time is by running 'sudo badblocks /dev/sda -w -s -p 5', this command may take a very long time.
Code:
sudo badblocks /dev/sda -w -s -p 5
After that, you can make a partition in your hard disk with QTParted and format it with a file system if you want to.
If you still can't get your Windows CD to boot, you'll need to either or go buy a new Windows CD or install Linux instead.
There are lots of good Linux distros now that are made for installing to hard disk and some of them are very user friendly these days, (more user friendly than Windows).

Regards, Herman