Recently I had an issue where aspnet_regiis.exe -i was not updating the home directory configuration for my web root in Windows XP SP2.
To resolve this I used the following commands, suggested by my colleague Mark Mann, instead to first remove all script maps to any version of ASP.NET from the specified path recursively, and then reinstall them.
C:\Inetpub\AdminScripts>aspnet_regiis.exe -k W3SVC/1/ROOT
Start removing any version of ASP.NET DLL recursively at W3SVC/1/ROOT.
Finished removing any version of ASP.NET DLL recursively at W3SVC/1/ROOT.
C:\Inetpub\AdminScripts>aspnet_regiis.exe -s W3SVC/1/ROOT
Start registering ASP.NET scriptmap (2.0.50727) recursively at W3SVC/1/ROOT.
Finished registering ASP.NET scriptmap (2.0.50727) recursively at W3SVC/1/ROOT.
This can be confirmed in inegmgr, by looking at the home directory configuration for your default web site.
