After playing some more, my sneaking is still working fine, but the Sneak-Eye is totally bugged. It just randomly shows "Detected" and "Hidden" sometimes around enemies, even when the enemies actually act differently...
I also noticed that the Dwemer Centurions are not attacking me at all on sight, they only do when i click E on them or attack them first... Maybe it should be like that in Blackreach, but i'm not sure...