Windows and Automated builds

We've run into a couple of interesting situations with Windows with our automated build scripts that I wanted to document. Both of them have to do with inconsistencies with what the Windows GUI is saying about a configuration versus what the operating system is actually using for a configuration.
Both of these situations were discovered while we were trying to do an expansive upgrade of our code to use the new .NET framework. In the first instance we were manually trying to install/uninstall dll's from the gac on a particular box. We manually dragged and dropped a particular dll into the c:\windows\assembly folder and the GUI would say everything was successful with registering the dll in the gac. However, check it from the command line, or try to run something in the application against the newly gac'ed dll and the OS didn't seem to see it. The only way we could get the OS to successfully see the change was to gac the dll from the command line.
In the other instance (which is sort of similar in nature), our automated deploy scripts are creating a Virtual Directory underneath an IIS web site on a remote server. After the Vdir is created, we had a 'step' that automatically updated the ASP.NET version on the Virtual Directory fo 2.0.50727 (C:\WINDOWS\Microsoft.NET\Framework\v2.0.50727\aspnet_regiis -s W3SVC/%WEB_SITE_NUMBER%/Root/%WebSiteName%). This script ran successfully, and the ASP.NET tab in the VDir on the web site displayed the change. However, IIS didn't actually see the change and continued to run the web site on the old 1 .1.4322 version - even though the GUI in IIS said it was. We knew this because the C:\WINDOWS\Microsoft.NET\Framework\v2.0.50727\Temporary ASP.NET Files folder didn't have the new corresponding virtual directory folder (this is where IIS keeps the compiled pages - it's like the 'working' folder in Tomcat). It seems the IIS metabase was updated, but the registry was not. I have a hunch that this might be because during that particular deploy, we left IIS running while we did the deploy. Perhaps shutting it down would make the update work properly through to the registry.