I was at a client today, working on a TFS 2008 cube corruption problem (I hate the super common code churn crap it always throws, requiring weird InstanceInfo and SetupWarehouse voodoo) when the subject of automating BizTalk 2009 projects came up.
The company heavily uses BizTalk, so they threw up a staging server with BizTalk 2009 on it and ran the Team Foundation Server Build Setup. After this, building non-BizTalk projects was working just fine, but BizTalk projects fail to build. After examining the box, they had copied various things from a BizTalk development workstation, but none of the additions had any effect. The rationale behind this was they don’t want Visual Studio on the staging server, but without it when running the BizTalk install the Developer Tools and SDK option is not selectable.
To get around this, look during the installation of BizTalk under Additional Software, and find the Project Build Component feature. While this allows for builds without Visual Studio, it should be noted that you can’t generate MSI packages, just build stuff.