Incompatibilities around BizTalk Server 2009
This is a quick post … after a lot of challenges with a recent deployment of BizTalk Server 2009, it is important to keep the following very much in mind.
BizTalk Server 2009 and SQL Server 2008 R2 are not the best match, work with SQL Server 2008 with SP1.
.NET 4.0 has the ability of breaking a not yet configured BizTalk deployment. Where? Enterprise SSO configuration will refuse to talk to the SSODB (mind you, the process will create the DB).
There are fixes for this last one, just make sure you are aware in case someone runs Windows Update or maybe it was configured to run automatically (not best practice to do this in production, but we are past that lesson 
).
The fix:
You will need to run regasm. The path to it? If you are working on a 64-bit system: C:\Windows\Microsoft.NET\Framework64\v2.0.50727. 32-bit would be here C:\Windows\Microsoft.NET\Framework\v2.0.50727. It is not just regasm, there is something you need to let it register.
Again, if you have a 64-bit system you will need to register both the 64-bit and 32-bit files.
32bit: regasm “C:\Program Files\Common Files\Enterprise Single Sign-On\win32\ssosql.dll”
64bit: regasm “C:\Program Files\Common Files\Enterprise Single Sign-On\ssosql.dll”
Also, you will need to update your Enterprise SSO.
More information on this can be found here: http://support.microsoft.com/kb/2252691/
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