As far as your "Start at Sea" option:
I've found that when I finish a patrol, refit, and am ready to start the next patrol, I have to
exit the game and
re-start it using SH3Commander for the start at sea option to work.
If I finish a patrol, refit, and am ready to start the next patrol, and
don't exit the game first, I start in port and have to work my way out again.
A pain, but I prefer the start at sea option as well due to limited time to play.
Hope this helps.