I don't want to fully blame this on Chunky, but I loaded a big part of a server I have with Chunky, and none of the spawners in the trial chambers work. They say they're inactive, instead of active/waiting for players. I've tried using the same server with the same plugins, just with the old world deleted and no chunks loaded with Chunky, and the trial chambers worked.

Chunky does not affect the behavior of Trial spawners. You can read more about how they work here. Inactive spawners are a game mechanic.

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