That would explain it then, changing people around. Unfortunately, the deck crew's clothing does not follow the characters, but rather their positions. The way the S-Boat crew is put together, there is not a CPO available for watch duty, so a regular PO is used instead. What the game does is use the position though, for the clothing change between Watch and Battle Stations. Therefore, the crew is "stripped" of clothing before deck watch, and then clothed for watch duty. When you moved one of the officer characters from inside, that 3D character happens to have a hat assigned to the actual character, otherwise you would only see the canvas cap of the 3rd Watch Leader's position:
Type= Leader
WatchIndex= 3
IDLinkCrewMember= POWatch
WatchCrewMemberSlot3D= WCS_03_dummy
...
WatchAccessoriesForAdding3DObjects= Binoclu_WCS, sapca_m#Head
WatchAccessoriesForSubtracting3DObjects= sapca_m01, ...
That "m#Head" is the canvas cap, and it goes with the "WCS_03_dummy" position. If you put the crew back, they will "clothe" fine.