This bug has been around for a while, but it is really awkward to deal with with. What happens is you get a Biome where all blocks that aren't like cobblestone are completely black. Please fix!
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It no longer is quite as bad, and now you can fix the rest manually as a player. I have added a screenshot of what is left.
Is this still happening as of 1.0.4.11 (1.0.4 official release) and/or 1.0.6.0 (1.0.6 build 1)?