There was an issue with 4.9 that was resolved with 4.10 that would sometimes cause the lighting build to never fully finish. It would complete the light build to 100% if you were to look at the Log in Swarm Agent, but it would never fully send the light build back to UE4. This was only under certain circumstances and largely depended on having a particular object in the scene or removing an object from the scene. Needless to say, there were multiple reason it could cause this.
If you have access to 4.10 I would highly recommend using that build since it resolved that frustrating light build issue.