The shader I use (Continuum 2.1 Alpha) marks glass as a translucent material in block.properties using:
layer.translucent = glass glass_pane

This is to apply refraction and reflection effects from the shader used on objects like stained glass on normal glass with the same code, as normal glass is not usually treated as a translucent material by optifine.

However, with this mod, the glass doesn't render at all, and appears completely invisible.
The only way to see glass again is to disable the flag in block.properties, however you lose the nice glassy effects.
Recreatable with:
Minecraft 1.12.2
BetterFoliage 2.3.1
Optifine F6_pre1
Continuum 2.1 Alpha

2020 me had no idea how anything works, closing this