And to that: To "remain" a captain or sorts, I just change my title and pins (bandolier, shoulders, etc.) to reflect that rank. It's possible to make yourself look like you are still a captain to other players.
Raising my hand and saying that I'm having this exact issue. My separation pets (saucers and runabouts) fly off into the distance. They are not invisible, but totally absent, rendering them useless. They can be called back, but serve no function and disappear into the distance as soon as they are released.
I've been having this issue with my saucer separation/aquarius escort as well. What is the name of the discussion in the bug section so I can post there too?
I just tested this out, and confirmed it. I still wish I knew of a way to fix it. I've been putting up with it for a year, and it's not easy to dig through the forums to see if this issue was taken up before.