If your win 2003 Domain Controller is running 100% CPU by System in the Process List.You have checked there is no network traffic outbound that is unusual.If you want to fix this problem try one of the following solutions
The cause for this problem could be with the CPQFCAC.sys driver (Fibre Channel Array notification driver) that causes this type of behavior. Historically the problem has been resolved by disabling the MSA1000 device in Device Manager (in the System Devices). However, HP has just released a new version of the FC Array Notification Driver which is supposed to resolve this issue and can be found here
Disabling the MSA1000 device will disable the receiving of MSA related hardware events (drive failures, etc.), so try to install the new CPQFCAC.sys driver.
If you are experiencing 100% CPU utilisation on a win 2003 file server and if you are using Trend OfficeScan ver8, go to the Officescan Web Based Management Console, and under Network Computers \ Global Client Settings, uncheck the tick box for Show the alert icon on the Windows taskbar if the virus pattern file is not updated after X days, that should solve your problem.