I took a look at the map, and you've managed to do something really crazy. Basically, all the normal brushes should be a part of the "worldspawn" entity, and that should be the first entity in the game. Somehow you've managed to make the worldspawn entity not the first entity, so it messes all kinds of things up. I didn't even know that was possible to do. I'm surprised the game runs at all.
At this point, you might be best off rebuilding the map from scratch, and don't do whatever it is that you did to the worldspawn on the new one.
Also, it would allow you to construct the map properly with good grid alignment.