Recently Microsoft released Service Pack (SP) 2 for Windows Server 2003 (http://www.microsoft.com/technet/windowsserver/sp2.mspx). We tested ISA Server with the Windows service pack quite extensively. Unfortunately we discovered after the release of the Windows service pack that there are several issues that have potential ill-effects on ISA Server. This blog summarizes the currently known issues, and suggestions on how to mitigate those issues.
1. If you run ISA Server 2004 Enterprise Edition with or without the ISA Server SP2, you must install ADAM SP1 on the ISA Server Configuration Storage Server prior to installing the Windows Server 2003 SP2. ADAM SP1 can be downloaded from http://www.microsoft.com/downloads/details.aspx?FamilyId=9688F8B9-1034-4EF6-A3E5-2A2A57B5C8E4&displaylang=en.
If you install Windows Server 2003 SP2 without first installing the ADAM SP1, ISA Server will not start after the installation, and you will have to uninstall Windows Server 2003 SP2. Further information is available in the Windows Server 2003 SP2 release notes, at http://technet2.microsoft.com/WindowsServer/en/library/ed5382af-e819-4d33-ace0-225d31b7ab751033.mspx?mfr=true .
2. If you run ISA Server 2000, 2004 or 2006 Standard or Enterprise editions on a multi-core / multi-processor 32-bit computer, and the CPU is heavily utilized, you might experience performance degradation in certain deployment scenarios after installing Windows Server 2003 SP2. The issue stems from a change in interrupt handling introduced in SP2.
To correct the issue you must download and run the Interrupt Affinity Tool (intfiltr) available in Windows Server 2003 resource kit (http://www.microsoft.com/downloads/details.aspx?FamilyID=9d467a69-57ff-4ae7-96ee-b18c4790cffd&DisplayLang=en).
You can read about installation and usage of intfiltr.exe in http://support.microsoft.com/kb/252867.
3. If your network adaptors (NICs) support receive-side scaling (RSS), then in certain NAT scenarios ISA Server 2000, 2004 or 2006 Standard or Enterprise editions might not transfer packets from one NIC to the other after installation of Windows Server 2003 SP2.
To correct the issue you must disable RSS support - follow the instructions in http://support.microsoft.com/default.aspx?scid=kb;EN-US;927695.
ISA Server Sustained Engineering Team