The problem is when you create a "empty world" when you generate a superflat world with the preset "3;minecraft:air;0;village" It only happens when you have the block set to air.
Environment
Operating System: Windows 10
Java Version: 1.8.0_25
JVM Arguments: -Xmx4096M -Xms4096M
Is this still an issue in 15w44b? If so, please explain the issue in detail and provide steps to reproduce it.