After installing ASP.NET 2.0 on a box that hosts MCMS 2001 with Site Builder Refresh Site Builder Refresh will no longer work.

To resolve this problem it is necessary to create a NRClient.exe.config file inside the C:\Program Files\Microsoft Content Management Server\Client directory with the following content:

<?xml version ="1.0"?>
 <configuration>
    <startup>
         <requiredRuntime version="v1.1.4322"/>
         <supportedRuntime version="v1.1.4322"/>
     </startup>
 </configuration>

This is officially documented in the following KB article: http://support.microsoft.com?id=916132