<p>We are attempting to install BizTalk Server 2006 R2 on a fresh server with x64 Windows 2008. The basic configuration is complaining that the “Default Web Site” we select for the BAM Portal installation is not validated due to “IIS is not 32-bit enabled.” Despite setting the appPool (Classic mode) 32-bit property to True, BizTalk configuration wizard is still complaining.</p>

<p>Has anybody successfully installed BAM Portal in 64-bit IIS 7.0?</p>

It looks like Microsoft’s official statement is Biztalk Server 2006 R2 with Windows 2008 is “not supported”. BizTalk Server 2009 is the one that is meant to be married to Windows 2008.
UPDATE, MOFE INFO
I should additionally comment that the process of
setting up a multiple servers for a BizTalk Group
requires configuration of network COM+ and DTC access, of which Windows 2008 interface of doing so differs from Windows 2003. In fact, I haven't found how to configure MSDTC in Windows 2008 as required by BizTalk 2006. Failing to properly configure this will prevent some of the databases from being created properly in a remote SQL Server due to transactional failure.