FIX: You experience various problems when you develop a BizTalk project that references another BizTalk project in Visual Studio on a computer that is running BizTalk Server 2009
If when developing BizTalk 2009 solutions (Orchestrations) and have split the schemas out into alternative assemblies (projects) – sometimes you’ll get odd not found issues with some (if not all) of the types in those referenced assemblies.
Solution is this hot fix -
http://support.microsoft.com/kb/977428/en-us