I believe the **.* is acting as a crutch for your NCrunch build, allowing it to work in situations where probably it should be failing consistently .. That's a theory anyway :)
Would you be able to copy/paste the MSBuild output leading up to the SGEN failure?
Something else you can try is to set
CopyReferencedAssembliesToWorkspace property on all of your projects to TRUE. This will help us identify whether the SGEN problem is a symptom of a dependency resolution issue.