The problem with settings is that they are saved to Atlantis3.cfg, but are then being read from Atlantis4.cfg, due to a typo(?) in the .exe file code. Both of these options are confirmed to work.
This bypasses the problem, but needs to be repeated whenever any game options are changed.
This actually fixes the .exe, and so never needs to be repeated.
34 2E 63
33 2E 63