I was torn between posting here and the actual tools forum... The Tools forum seemed like it was only for posting the actual utilities and not Q&A about them... (please move if I am incorrect)
I have a private server for my friends and myself, and am planning to create a large dungeon for them to explore. The dungeon will be housed within a shell of bedrock and each floor/ceiling will also have bedrock insulation. To speed things along, I used an editor to quickly hollow out a massive cube several meters underground and generate the empty levels within the cube. Each floor consists of a layer of smooth stone, then bedrock, then smoothstone again (serving as the ceiling for the level below).
I used the latest version of Axialmedia's Minecraft Editor v1.8.0 [link] which is compatible with the current minecraft version.
Upon re-entering my world , I find that every level of my "dungeon" behaves as if it is exposed to open sky. Despite the fact that there are several layers of unedited dirt and an entire cathedral sitting on top of the underground cube (and the cathedral's lighting behaves as it should). Also despite the aforementioned smoothstone/bedrock/smoothstone divisions between each level within the cube. Adding/removing torches doesn't kick the lighting engine into recognizing the obvious opaque blocks that should be blocking all sunlight.
What's going on? And more importantly, how can I fix this?