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.
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Is this still an issue in 15w44b? If so, please explain the issue in detail and provide steps to reproduce it.

It's not an issue in 15w44b. It must have been fixed around the time they added "The Void" preset.

Fixed somewhere between 15w34d and 15w44b.