I have no idea if this is an Atum bug, but I've had lighting bugs occur, where it is pitch black dark, and it even works as if it's dark.
How to Replicate:
1: Set a bed in Atum, make it as your spawn
2: Go far enough to unload the chunks
3: Die
That's what I'm suspecting makes it happen, you might have to go far.

Note the stoneguard in broad daylight, that spawned in the dark, along with some undead that spawned that are currently off screen

Could you provide the world & coordinates to the place where it´s happening? :) Sounds very weird!

Closing because of lack of response.

Closing because of lack of response.

Gah! So sorry! It's happened across many worlds for me, but the seed for this one is -3457347346652005390, coords being X69.8.09, Y66, Z-276.

Unable to reproduce it with the same seed, following the instructions. The structure is there though, but no lightning issues.