I recently installed BizTalk 2006 and 2009 on a few servers at work. I found the process to be very painful for some reason.
In regards to the BizTalk 2006 installation, I was running into an issue where the installer would error out. I eventually tracked it down to my Virus Scan software blocking the installer from stopping the WMI service on my server. I would recommend disabling virus scan software during the installation. This same issue will also affect the installation of BizTalk 2009.
For my BizTalk 2009 installation, I thought it would be smooth sailing after figuring out what was wrong with the 2006 install, but I was wrong. After the installation, I launched the configuration console. I noticed that I was unable to configure SSO because it said it could not find the database on the SQL Server. Since I had not yet created the database, it was correct for it to not be there. After nearly half a day of troubleshooting, I discovered through different online posts that you have to manually register the SSOSQL.DLL with both the 32-bit and 64-bit .NET framework.
C:\Windows\Microsoft.NET\Framework\v2.0.50727\regasm “C:\Program Files\Common Files\Enterprise Single Sign-On\ssosql.dll
C:\Windows\Microsoft.NET\Framework64\v2.0.50727\regasm “C:\Program Files\Common Files\Enterprise Single Sign-On\ssosql.dll
After fixing the SSO configuration, I ran into an issue configuring the BizTalk Groups. This was an easier fix. You must ensure that Remote DTC is enabled on the server with all of the options checked.
Once all of this was in place, I was able to get BizTalk 2009 up and running in much less time.