We've been trying to make a more efficient wither hunting area, so you don't have to run up and down stairs and through small corridors etc. There is a lava lake under all of that, but about 40-50 blocks below. I've completely removed all the nether bricks in those areas and there is no hidden lava or glowstone or anything.

Also weird is that a few of these areas, if you just stand still in the middle of the light for between 5-30 seconds, sometimes (but not always) the lit up floor will go dark. But if you leave that spot, about 30 seconds later it lights up again.

Oh and some of these lit up areas are directly above pillars, so even if it's the lava ~40 blocks below, how is it transmitting through the pillars that far? And why isn't the whole floor lit up?

And I have seen this happen in other non-modified fortresses as well.

Steps taken to try to fix -

1) Remove all bricks, replace. Problem returns.

2) Place bricks on top of the light sources. Limited success, sometimes it makes the area go dark, sometimes the next level up becomes lit.