Ugh. I wished you had asked just last week. --wry grin-- As I'd spent three hours trying to fix that. I did exactly what people had said to do in threads: edit the crew position numbers, ect ect ect to get the 'missing' officer back out of limbo but it didn't work. I wound up restarting things two patrols back just to get him to reappear.
Tell ya what: I'll experient some the next coupla days and see if I can get that to replicate again. If I manage it I'll let you know.
Real quick though: was this ever a problem before people used Commander? Only reason I'm asking is to start trying to figger out variables, and one of them is is whether mixed-starting might be part of it.