The world doesn't sometimes generate fully, often just one chunk in the middle of the world is missing. You already loose life if you just walk very near to the chunk (actually partly over it by pressing shift). If you walk down the cliff you fall through Y=0 and die very quickly. But rain collects on the ground and no water or lava is able to drift into that chunk. Often the frame rate decreases very often near this chuncks. You can fix the problem by letting the chunk "regenerate" when you deleted it with e.g. MCedit. I played around with biome sizes Ore number and size and so on, it may be because of this feature.
I will also report another bug later about 2D trees and non-generated buildings later.

What I expected to happen was...:
All chunks would be generated the first time.

What actually happened was...:
Some chunks only generate if you deleted the corrupt ones again.

Steps to Reproduce:
Sadly not always reproducible:
1. Set the world attributes (I mean biome size, ore generation, etc...) to non-default values
2. Run around and let the world generate until a chunk is corrupt