I compiled and got the same lighting results. I tried tweaking some of the levelflag settings to see if it helped, but on recompilation the bottom is still lit up. I'm not sure why this is happening. Hopefully mattn or someone has some ideas...
Also, I noticed you have a lot of windows as func_breakables. This is, of course, very cool. Unfortunately, for now func_breakables cause considerable lag in our pathfinding. This is why your map takes so long to load. And if you try to shoot them out, you'll probably notice a signicant pause as the pathfinding is recalculated.
Maps can take a few func_breakables, but not so many as you have. I would recommend using windows that don't break for now. If we ever get the pathfinding/func_breakables issue worked out, we can always turn them into func_breakables later.