The crew remaining on deck when submerged is because of Alt Tabbing. It doesn't have anything to do with the sub crew load out. This used to happen to me and was pointed out in another thread. Once I quit alt-tabbing no more outside crew. It is just a graphical anamolly--all the crew are inside at their stations. Also, if you alt- tab you will disable your ability to go into silent running. When you need to go to the Desktop, save the game and go to the Main Menu. From there you can alt tab to the Desktop with no problems (that I know of) and it is a quick return to the game from there.
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