Microsoft is aware, through recent customer feedback, that some enterprise customers have been experiencing performance issues when they apply Microsoft updates to certain workstations or servers. Customers are experiencing this when they use Microsoft System Management Server (SMS) 2003 Service Pack 1 (SP1) or a later version together with the Inventory Tool for Microsoft Updates (ITMU). Customers also experience this issue on computers that are running the Windows Update Agent (WUA). The performance issues are causing high levels of CPU consumption when the customers perform a scan or when they apply Microsoft updates.
See full Microsoft KB: http://support.microsoft.com/?id=924148