<snip>
...I replaced my cdrom reader with a new Samsung 48x cdwriter ...
</snip>

Check in your BIOS to make sure that DMA is turned on and that the boot order is correct. Windows can override BIOS DMA settings, but I'm not sure about Knoppix.

Another thing to check: make sure that the CD burner's firmware (internal BIOS) is up-to-date. It's not unusual for there to be a revision available, even in a new drive. You can check this from Windows using Device Manager; bringing up the Settings tab from the Properties selection of the menu for the CD-ROM drive will show the firmware version. Check this against the Samsung website.