Even though the Security Update 11-04-2003 is included in the OS X 10.3.1 Update, some users may want to install the Security Update without upgrading to 10.3.1. We previously covered problems installing the Security Update, along with a few user-provided workarounds. Yesterday Apple released a Knowledge Base Article documenting these installation issues and providing an official workaround.
According to Apple, the Security Update may fail if you have more than one application on local hard drives whose names contain the word "Terminal." The workaround, explained in the article, is to use the Finder's search command to search Local Disks for items whose "Name contains Terminal" and whose "Kind is application." If you find any other applications on local disks with "Terminal" in their names, rename them in the Finder. (Apple suggests simply removing "inal" from the end of the word "Terminal.") You should then be able to install the Security Update. (After successfully installing the update, you can restore applications to their original names.)
To reiterate, if you've installed the OS X 10.3.1 Update, you don't need to install Security Update 11-04-2003.