Possible wrongful time simulation on server

Sometimes, immediately after I join my server.

I hear a lot of thunder simultaneously if I'm underground. 

The latest occurence, I also a lot of mobs in my spawner (as many as if I AFK for about an hour) despite killing all mobs before I left. I checked the console and nobody joined between the two times. I wonder if the server is simulating time strangely?

Causes many fires all at once from so much lightning.

 

EDIT; the woodland mansion was already burned down separately from the glitch 

EDIT 2; mob farm not in spawn chunks and THIS GLITCH DOES NOT OCCUR EVERY TIME