After some testing, it appears that it's not a problem with your mod. The firefly systems are getting killed because they contain both an init emitter that doesn't loop and a regular one that does, and when the init one finishes the whole thing gets culled. It's a bug that must have been introduced when trying to optimize particle systems. It may also be affecting other systems that are built in the same way, but I can't think of any off the top of my head.
I've remade that particle with the init emitter and continuous emitter in different systems, and that fixes the problem. You can add it to your mod, it will have the side affect of fixing all the fireflies in the mine and in town as well:
fireflies.layout