Think I found what I need for MD5summing on NTFS for windows. It is called MD5Summer available Here
It will even let you md5sum cd's and it will be saved in a format compatable with linux md5sum for comparing.

The way I think I will use it; md5sum the windows/system32/drivers directory, the windows install disk of the same files, fire up knoppix, md5sum the ntfs volume directory windows/system32/drivers.
Now compare the Knoppix md5sum (1=w/s32/dr, 2=active win version w/s32/dr, 3=install disk versions) 1>2, 1>3, 2>3.
I hope this will make visible anything lurking.

If this is valid for discovering file discrepencies, your comments would be appreciated.
If there are other methods available through Knoppix I would appreciate those comments as well.

Thanks,
Condor