I have been having this issue since I tried enabling random-light-updates sometime several months ago. I posted it on the spigot forums but never got any reply.

Basically, whenever random light updates are enabled, and chunks load (it seems to be in certain areas but they are very numerous, probably areas with lighting issues or something like that) then the server freezes and often crashes.

Prior to 1.12.2, disabling random lighting updates solved it. After getting 1.12.2, earlier on we had issues where many people got timed out while chunks loaded when they joined, and after many hours of trying to fix it, reverting to 1.12.1 fixed it. Later, I tried 1.12.2 again, and nobody seemed to have the issue anymore, but then we had the same issue we had that random lighting updates caused.

I didn't realize this connection completely until, while trying to find the cause of being unable to update to 1.12.2 without issues, I reset the spigot.yml and bukkit.yml and disabled all plugins. Of course, this did not help at all, but when I opened spigot.yml, I noticed that there is no more option for random-lighting-updates. This makes me think that those are always unchangeably on in 1.12.2, which perfectly explains all the issues we've been having.

PLEASE help me with this, our server is very far behind in terms of versions now and we can't upgrade past 1.12.1 without getting this fixed.