I just tried opening the administrative console and out of nowhere got an error "root element is missing (c:\Documents and Settings\user1\Local Settings\Application Data\Microsoft Corporation\Microsoft BizTalk Server 2006\Microsoft.BizTalk.Administration.Snapin.dll.config)".

 To resolve this issue, delete this file:

c:\Documents and Settings\user1\Local Settings\Application Data\Microsoft Corporation\Microsoft BizTalk Server 2006\Microsoft.BizTalk.Administration.Snapin.dll.config

The next time you start the BizTalk Server 2006 Administration Console, the Administration.Snapin.dll.config file will be auto created for you.

Cheers.