I've found a big incompatibility. It is with Realistic Terrain Generation mod. When I generate a world with it (it has specific world type also) your levels don't generate as they are intended. I spawn in a small room at the top of the world. Each level is simply filled with stone and rare caves/mineshafts. If there are special ores/resources - they are embedded in stone.
But if I generate a Default type world, vanilla - levels generate just fine, as intended.
I tried your mod in it's latest version and RTG of 126.96.36.199 and 188.8.131.52.
Please, take a look into that.