Resetting the engine causes the workspaces to be purged, with new ones created as the projects start getting built. So I don't think it was removing the workspaces that actually solved this.
I think this might actually be something in the source code itself that eventually reset itself, perhaps one of the MSBuild dependency cache files. If you see this again, I'd be interested in knowing whether doing an MSBuild clean then a reset of NCrunch makes it go away.