In my windows 2003 server standard edition, the CPU usage is always 100%. The only application running is Ciscoworks LMS 2.5. There is adequate RAM and Hard Drive space. Any idea why this is happening. I have killed all the unwanted processes like Java, etc.

Check ALL background processes running. There is probably one that is taking up most of the CPU and it may be a trojan or key logger.

I would run Ad-Aware, Spybot and then Norton to ensure that you don't have a virus of some sort.

Did you install software and didn't complete it? Did you reboot?

Is this server on a domain? I would check to see if you are behind a firewall as well.

I have Trend Micro OfficeScan running in my server. It is a workgroup server running out of VMware. There is no firewall. I ran Ad-Ware before and that was the first thing I did to eliminate the issue.