I have found a little quirk with using SH3Commander and WAC. If I save a game and then reload it (assuming I don't get a CTD doing so, of course!
) some of the options do not carry through. So far they seem to be the "Gameplay Settings" ones.
For instance, if I have a fatigue model chosen, I experience crew fatigue up to the point of save-and-reload, at which point fatigue stops. If I have chosen to hide hull integrity, I do not see hull integrity up to the point of save-and-reload, at which point I can now see hull integrity again.
I have no idea about other "Gameplay Settings" options, like "Model effects" and "Randomise U-boat crush depth", since they are not easily changed-identifiable or -detectable while playing.