Consider the following scenario. You have custom HTTP headers configured for your IIS 6.0 Web site. By default, these custom headers get inherited to the applications or virtual directories underneath this web site. However, you have specifically removed these headers from the application or virtual directory levels. You run aspnet_regiis.exe with the install (-i), uninstall (-u) or repair (-iru) switches. During the aspnet_regiis.exe routine, your custom HTTP headers will be added back to the applications or virtual directories in question. These newly added headers are essentially the headers that are present at the parent web site level.
This behavior only occurs on Windows Server 2003 running IIS 6.0. Simply remove the unwanted headers from the application or virtual directory configuration if they re-appear after running aspnet_regiis.exe.