The issue was already in our WIndows 2003 Server, We created some new VMWare Servers with Windows 2008 and migrated the active directory roles and deleted the old Server so now in Our AD run only 2 Windows 2008 servers. in VMware with 2 processors each and 4GB ram.
The CPU goes 100% and the process that uses it is the System process. When we restart the Servers, the CPU remains low, but after a couple of hours increases again to 100%. This happens in both servers. The only thing we are doing in AD, is assigning Printers and Shared drivers to the users via a self created script in c# which run through AD: I would really appreciate your help in first locating where the problem is and than fixing it.