Hey,
sorry for the necro. I have this exact same thing and this is one of the few bug threads that talk about slow mode. Slow mode does not seem to work in the Thaos fight for me, but works everywhere outside. I only noticed because i finally finished a solo pacifist cypher today, which required a bit of micro managing in the last fight, which was slightly elevated in difficulty this way. Now I am not sure if it's the same bug, because OP wrote about auto slow-mode only and I'm not sure if setting it manually to slow mode also did not work for him/her.
Just to clarify: Even while it prints "slow mode active" on the screen in the thaos fight, the speed is still normal. Current version is: 3.06.1254 (fresh install).
