Erm, I may have just found a genuine bug! So I was playing last night on my laptop from scratch. Reached my first SA reset and logged off not long after. Today I've opened the game and the SA and Automation tab has gone and Particles are no longer generating despite me having plenty of Quarks to be generating them. I also still have the SA achievement so the game does "know" I've got that far.
Tried closing and re-opening the game, but no change.