BizTalk Server 2006 R2 does not compatible with Windows Server 2008 and SQL Server 2008.
I setup BizTalk 2006 R2 on Windows Server 2008 (64bit) with SQL Server 2008(64 but), and tested with a simple publish-subscribe application, it seems work fine. But Microsoft states that the compability issue of BizTalk Server should be fixed on BizTalk Server 2009 which should be released around 2009 Q1.
I even try to user Visual Studio 2008 with BTS 2006 R2 (64 bit with Server 2008 64 bit,SQL 2008 64 bit), and sadly find out that VS2008 simply can not recognize BTS 2006 R2 Project file. This should also be fixed on BTS 2009.