It seems as if every chunk I log into is affected by a glitch that ignores blocks above and allows sunlight to pass through. I came across this when my skeleton farm stopped spawning in the day time (a skeleton even burned up underground), and my slime spawn started spawning like crazy in the day.

Logging into a world and going in spectator revealed all caves to be dark as they should. But if I go into the cave, log out, and then log back in within that chunk, then the lighting will be as if sunlight reaches it.