Pregenerating a world (Chunky) with Panthalassa on apparently causes a thread lock, related to Panthalassa's structure processors:
https://github.com/Sniffity/Panthalassa/blob/master/src/main/java/com/github/sniffity/panthalassa/server/world/processors/LaboratorySupportProcessor.java#L53

Pending investigation as to why this might cause a thread lock.