Recently I had some trouble when I wanted to create a new orchestration in Visual Studio 2008. The template for the orchestration was gone while the other templates (schemas, maps, etc.) where visible:
I could easily fix this by repairing the BizTalk installation but I must say I do encounter more strange problems with BizTalk 2009 and Visual Studio 2008. It looks like fixes and patches to VS mess up the BizTalk 2009 functionality.
This is probably related to the problem (and solution) described in Matt Milners post. I didn’t try it but I think Matt’s registry solution would have also fixed the issue above.