No startup after attempted download of sketchup

I clicked run instead of save to download sketchup. The screen saver went on while I was busy elsewhere and when the estimated time of download was almost up I shook the mouse to log on and when I did the pc rebooted to a black screen that said "windows could not start because the following file is missing or corrupt: \Windows\system32\config\system. It says I can attempt to repair this file by starting windows setup using the original setup cd rom. Select r at the first screen to start repair.

This dimension 4100 originally came with mellenium. I bought an xp home upgrade, deleted the hard drive and did a clean install. I've never had a problem. I'm lost here and would really like to get my pc back as I need the auto cad lt that's in it. Thanks