MS 2003 Server

Every once in a while my W2K3 server acts up (will not let me open programs) so I reboot it. Every time I reboot this server, it gives me an error that I have a corrupt or missing config.sys file. So, I insert the CD and run chkdsk /r from the console. I had to do this twice in a row, until I added more RAM. Now it’s only once. After it repairs, it boots up fine — until the next time I have to reboot. What is going on, and how can I fix this problem?