Steps to Reproduce:
1. Create a superflat world.
Observed Result:
1 - Random chunks were generated with regular world terrain, not flat.
This seems to be a very rare bug. (These kind, I hate, since it can be a number of combinations). I had the render distance set to 32 chunks, but future superflat maps with 32 chunks loaded (same and different seed) didn't produce the bug. I also tried recreating the world with the same name (I've seen this happen before), and creating a custom generation world prior to the superflat world, but also didn't reproduce the glitch.
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It could be the old and kind of tricky to get Chunk Resets which, from what I remember, use to reset the chunk if an invalid block was created/loaded. This is most likely fixed but it could be a possible explanation.