One of error I received while configuring "Windows SharePoint Services Adapter" for BizTalk Server 2006 is as follows -
Error Msg - "The website selected is not configured with the expected ASP.NET version. The expected version is 2.0, the actual version is 1.1 (CWssadacfg)".
I had both versions (1.1 & 2.0) installed on my box. When I opened IIS Manager to check the version of the selected website - I could not see the ASP.Net tab where you select the default framework version to be used for the website.
My Resolution -
I reinstalled ASP.Net 2.0 with command -
"%SystemRoot%\Microsoft.NET\Framework\v2.0.50727\aspnet_regiis.exe" -i
This resolved my problem. However, if this does not work for you then you may try forcefully upgrading SharePoint by -
"%CommonProgramFiles%\Microsoft Shared\web server extensions\60\BIN\STSADM.exe" -o upgrade -url http://localhost:80 -forceupgrade
More info about STSADM.exe - http://technet2.microsoft.com/Office/en-us/library/188f006d-aa66-4784-a65b-a31822aa13f71033.mspx?mfr=true