When using block.setBiome() or World.setBiome(x, y, z, biome) the block that is updated isn't in the same location as the one specified.

Here is an example of some dummy code used to test this:

Block block = event.getClickedBlock();
Location loc = block.getLocation(); 
loc.setY(0); // Set Y to 0 so it appears/updates in-game
loc.getBlock().setBiome(Biome.JUNGLE);

When a block is clicked, a different area of the chunk changes biome. For example, when clicking the blue carpet in the attached image, the biome changes in the area that's circled red.

I have attached a plugin that replicates this - if you right-click the ground with a stick it will change the biome to Jungle.