When generating a world with the customized world type, some chucks can generate incorrectly, reminiscent of what would happen if you generated new terrain using beta 1.8 an older world. The incorrect chucks seem to only generate near your spawnpoint, farther away, they stop. This bug seems to happen in around 1/10 of the worlds generated. The world type only has to be "customized" for this to occur, you don't even have to change any of the settings. This happens inconsistently, if you generate a new world with the same seed and settings, it might not happen.
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Did you create any worlds using the same name earlier?
kumasasa
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In my original testing, I just left them all as "new world". After seeing your comment I tested some more using a new name each time, and that did seem to prevent the bug from happening.