Background- I installed multiverse on my server and created another world (/mv create Freebuild normal) for players to build in while the Main world is for players to battle gyms in and is completely custom and therefore does not contain all of the biomes that certain pokemon spawn in.
Problem- Pokemon do not spawn in the Freebuild world but they spawn just fine in the main world.
Plugins-
NOTE- I asked Cauldron and Pixelmon about this issue but they said this was a bug with forge not registering spawned entities in another world.