A few users have reported this configuration issue when trying to install and configure BizTalk 2006 with Windows SharePoint Services adapter. BizTalk 2006 native adapter for Windows SharePoint Services requires .Net Framework 2.0 but most of the users don't realize this until they try to configure the Windows SharePoint Services Adapter Web Service feature of BizTalk 2006. At that point, in many cases, Windows SharePoint Services has already been configured to run on top of .Net Framework 1.1 so the following error is visible in BizTalk configuration Web site is not configured to use .Net Framework 2.0
Changing the ASP.NET version on IIS site to be 2.0 instead of 1.1 causes Windows SharePoint Services 2003 to stop working completely.
This is not a BizTalk 2006 configuration issue, but BizTalk requirements combined with the succession of installation and configuration steps makes it pretty likely to run into this configuration issue of WSS 2003 with SP2. This is a known WSS 2003 with SP2 configuration issue and can be fixed easily by running STSADM tool with the force ugprade parameter.
In order to quickly upgrade your IIS site and WSS 2003 with SP2 from .Net Framework 1.1 to .Net Framework 2.0, run the commands below:
"%CommonProgramFiles%\Microsoft Shared\web server extensions\60\BIN\STSADM.exe" -o upgrade -url http://localhost:80 -forceupgrade