Enigmatica 6 -- V. 4.10

Certain biomes, or perhaps biome groups, wont generate Apotheosis structures.

For example, in desert-type biomes, it seems to be impossible to locate boss chambers/dungeons and rogue spawners (the ones with blocks above them and vines surrounding them)

The best way to figure out if a biome is generating them, is to go into spectator mode, and give yourself night vision. When flying around the caves, you should be able to spot them fairly quickly if they generate in the biome your currently in.

The biomes that I've had issues locating structures in so far are:
-Jungle type biomes
-Desert type biomes
-Ice type biomes

I'll add more to this list as I find them. I should also mention the world type I have tested this on is the default option. I haven't checked other world types yet, as I usually use default. This doesn't appear to be an issue with Apotheosis directly, as a testing modpack I have with a few other mods, seems to generate structures from Apotheosis just fine.

Thank you for the report, I will investigate the issue.