Refer'd Issue:
TwelveIterationMods/Waystones#415

Minecraft: 1.12.2
Forge: 14.23.5.2854

Mods: 4
EmbersRekindled-1.18
jei_1.12.2-4.16.1.302
Soot-1.10-hotfix
Waystones_1.12.2-4.1.0

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For some reason the Alchemical Recombulator, should it render causes the Waystone's Texture to turn dark. It appears to depend on what angle you look while looking at them.

Unsure if other particles/textures from Soot can cause this to happen as well.