Everywhere I go now, the first thing I do before I do anything else, is install these two hotfixes. They solve a bunch of extremely painful BizTalk 2009 development issues.

BizTalk Server 2009 Orchestration Designer incorrectly indicates that there is an error in a BizTalk Server 2009 project http://support.microsoft.com/?kbid=979153

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
http://support.microsoft.com/?kbid=977428

One gotchya to watch out for is that if you do a repair of either BizTalk or Visual Studio, (or in our case recently, reinstalled VS2008 SP1 in order to get the TFS client working) you will have to reinstall these hotfixes as well.