Cannot Find System.ini

Hi,
I went to a clients office to investigate why they only had half the icons on the desktop on Monday that they had on Friday. It did not appear to be the nimda virus so I continued. I ran scanreg /restore and took it back to Friday. When I rebooted the message cannot find system.ini you need to run windows setup again to install the file.
I sys the c: drive from floppy disk and still no luck. What can I do next?
Thank You