Yes, SH3 Commander will (potentially) change the malfunctioning parts of your boat
every time you launch the game with SH3 Commander.
So one day you couldn't go to ahead flank. When you exited and later started the game with SH3 Commander, it would have reset the malfunctions (and possibly created new ones) and applied those to your boat. So that's why it was 'fixed' later on when you resumed your career.
This is why I think it's best to only launch with SH3 Commander at the beginning of your patrol. It applies all those 'random' settings into the game files, and those will remain part of your SH3 installation until you use the 'rollback' option in Commander. (Or until you launch with SH3 Commander again, which will overwrite the random settings with new ones).
So maybe you should recreate that original SH3 desktop icon and use that to launch the game at all times except when starting a patrol. Otherwise you're going to find that different parts of your boat malfunction each time you reload the game (not every time, but sometimes). Hope that makes sense :hmm:
That's what I'm going to do, anyway
