I found the cause of some of the maps going black. It appears that these maps go dark because the map maker never actually put lights in the map. Instead they tell the map to tell the server to enable cheats and then to force sky light. Logically this causes serious security problems and the server to get hacked. New security plug-ins in the server prevent cheats being enabled and therefore prevent these map hacks from turning the lights on. As a result the maps will be dark until the lazy map maker releases a version that does enable servers to be exploited.