Paul Thurrott from WindowsITPro wrote :
Microsoft has published a list of 14 server applications that are incompatible to various degrees with Windows Server 2003 Service Pack 1 (SP1), confirming fears that the low-level security changes in Windows 2003 SP1 might cause problems. Most surprising: Many of the affected applications are from Microsoft.
In the Microsoft article, "Windows Server 2003 Service Pack 1 application compatibility" Microsoft describes the server applications it tested, then lists the ones that have incompatibility problems under SP1. Among the applications that have problems are Microsoft Application Center 2000 SP2, Microsoft Exchange Server 2003, Microsoft ISA Server 2004 Standard Edition, Microsoft Baseline Security Analyzer (MBSA) 1.2.1, and Microsoft Systems Management Server (SMS) 2003.