JS, I've only seen the missing Officer from the Repair section. In my case he was left in the Repair section upon returning to base by mistake. All the crewmen left there showed in the fore and aft bunks when leaving for the next patrol. Same for all subsequent patrols with crewmen. I've only just aquired the new Officer recently and made sure he was not in Repair when I docked. He's now on his 3rd patrol.
BTW, I only picked the 5th Officer while in a type IX/B. New one is in a IX/D2.