This is the big one. Glowstone was designed to be a native implementation of the Bukkit API (back when it was still on top), and I assure you that that API, and

This is the big one. Glowstone was designed to be a native implementation of the Bukkit API (back when it was still on top), and I assure you that that API, and thereby every plugin built against it, makes some heavy single-threadedness assumptions. Even if you conceive an API from scratch, Java hasn't the tools to prevent plugin authors from doing things they shouldn't in this regard.