I very recently had similar issue!
When I made a new map version (copy paste, change name, change name in map descriptions) it magically started working.
Also it was not a problem for the person I played with before new map version, only for me. I considered doing a "fresh install" to see if that solved it, but because it already solved itself, I never did.
The effects I had issues with where "Birth-only" special effects (Like explosions, blizzard, and such). "Lingering" special effects such as triggered projectiles etc. wasn't a problem for me.
Big mix of imported and vanilla vfx:es.
Game version 1.31