Curiouser and curiouser.
I don't know the tool you are using - can it not be made to say more - any clues
as to what and where the "unknown" files are ?
Meantime its possible you have corruption in your file structure and I'd run CHKDSK
with both /r and /f flags. The scan may take a very long time - but don't use the
/c or /i switches in your circumstances.