It's handled by our package, when the package is loaded in to Visual Studio. It looks like we call ProjectCollection.GlobalProjectCollection.SetGlobalProperty("MyExtensionDirectory", ...) at that point. I wish I could hand you a simple, complete repro example; sorry!
I don't believe it's an issue with "Additional files to include". I found that if I hand-edit a project to add:
<PropertyGroup>
<MyExtensionDirectory>...</MyExtensionDirectory>
<PropertyGroup>
then NCrunch successfully builds & run tests, which is why I draw this conclusion.