I got into the Recovery Console (which got me furhter than the Command Shell)
From the Recovery Consol, I was able to delete the "Windows\Y" file and change the hidden attributes (I remoded the H attribute) and rename the other files (Windows\0, 4,6,8,9 and S).
Then I rebooted.
The renamed files were there, which I then deleted and strangely enough, the files Windows\S at 1.3 Gig and Windows\Y at 1.0 Gig had re-appeared.
I then rebooted.
Now, all files are back to where they were, they have a s h for attributes and they are all 1.3 Gig in size exept Windows\6 which is now 1.0 Gig (like the Y file before).