For some time now, I’ve been working with BizTalk Server 2009.  One of the major frustrations has been with the VS 2008 integration.  Project references between BizTalk projects wreaked havoc if you were working on a single developer machine with BTS installed.  Fortunately, Microsoft has released a hotfix for many of these issues [1].  If you are having issues within Visual Studio, you may want to try this hotfix.  Look for the link near the top of the document to request the hotfix.  I got an email with the link within minutes when I tried. 

Thanks to Bryan Corazza of Avanade for pointing out this support document.