I may, or may not, be having a Commander-related problem (the original question was posed here:
http://www.subsim.com/radioroom/showthread.php?t=168411)
My question about Commander is this: my understanding from having read the manual is that, if you've started SHIII using Commander then exit the game, you don't have to restart the game using Commander as until I rollback (either manually or automatically) the changed settings are stored.
If I start SHIII using Commander and once the game has loaded, but prior to clicking on mission start, I then exit the game then restart SHIII direct, are the Commander changes still saved?