So far I've seen this happen with two dimensions specifically:
- In the Alfheim dimension from MythicBotany, the LODs used are from the Overworld
- In the Otherside dimension from Deeper and Darker, the LODs used are from the Nether
I pregenerated a world on the server PC using Chunky, then generated the LODs on a singleplayer world using the same seed. Upon joining the server with the LODs from my singleplayer world, the aforementioned dimensions are using the incorrect LODs. In fact, folders for these dimensions are not being created.
Screenshots Provided.