SMS 2003: ITMU v3 requires two passes, two reboots, to deploy April 2010 security patches
We've been getting some calls about this one so I thought it deserved a mention here. If you're having some ITMU related issues with the April 2010 security patch install then you'll want to take a quick read of this one. Note that this issue only affects SMS 2003. Our currently supported products, ConfigMgr 2007 and WSUS 3.0, do not share this limitation
The Configuration Manager Support Team Blog : SMS 2003: ITMU v3 requires two passes, two reboots, to deploy April 2010 security patches