When updating from 1.3.1 to any future version, the biomes in already generated chunks are randomly swapped for other biomes. This occurs no matter how I try to update. If a new world is created in the newer version with the same seed, the biome issue does not occur. Attached are screenshots showing an example of the issue. The first three screenshots are from 1.3.1, the next three are from 1.5.0 in the same world. The next three are from the same seed, freshly generated in 1.5.0.

1.3.1

1.5.0 old world

1.5.0 new world

You can even see that in the bugged world, ice is forming on the shore. This is because the volcanic island beach biome turned into snowy hemlock forest, which is cold enough to freeze water.

I believe this is the same issue as #20, but that issue was closed without comment, and the issue still exists in the latest version.

1.4.0 changed alot with structures and biomes... Blame vanilla for this, I highly recommend a fresh world or new chunks.