Not all the settings on the Black Mesa tab in options seem to save. After restarting my computer, the “View Roll” “Auto Aim” and possibly the “Train Fail-Safe” settings all reverted to their defaults.
I’m having the same issue as well.
Speaker configuration under audio isn’t saved as well, it’s because windows_speaker_mode isn’t a visible DVAR in Black Mesa (or doesn’t exist, idk what version of the source engine is used). If you use headphones and don’t want to re apply that setting every time you start the game add “snd_surround_speakers 0” (no quotes) in your autoexec.cfg under \sourcemods\BMS\cfg\
Minor resurrection of this thread, just to say thanks to Pyroh for providing the answer to this. 