You need to download (and apply!) ISA 2004 Service Pack 1 (which was released back in March) to your ISA 2004 systems for them to work on Windows Server 2003 Service Pack 1. Click here to access the download link. Both service packs provide updates to improve the security and stability of the software.
Windows Server 2003 Service Pack 1 brings with it a number of new security features including Security Configuration Wizard(SCW) and support for remote access quarantine. John Howard's post links to a document that describes all.