Log here.

Both screenshots were taken on the same seed (359828297144159) at 0,0, with the same settings (Elder Prismarine Biome set to Rarity = 1). The first screenshot is only with Quark and AutoRegLib installed, the second is Quark and AutoRegLib + CaveBiomeAPI.

As best I can tell, this is because CaveBiomeAPI's underground biomes are treated as proper biomes, and is causing the method below to return false when it shouldn't.
https://github.com/Vazkii/Quark/blob/bb564ebabed12c1c2090792e1f1e43796f9c7266/src/main/java/vazkii/quark/content/world/gen/UndergroundBiomeGenerator.java#L48-L51

There may be similar issues when dealing with vanilla cave biomes in the future. Replacing line 49 with something like this seems to fix the problem when I tested it, but I didn't think it was pull request worthy:
Biome biome = getBiome(world, pos.up((64-pos.getY())));