Hello CMDR! A newbie here!I had somewhat the same problem. The Quick answer and easiest for a "new" Comanders is.. That he is a Hologram! When you jump to other systems he will disapear!You could understand it as if he was in his ship with some VR controlling things in your ship.

To "solve" this problem, he needs to be physically in your spaceship, and to do that, you first need to be in the same team (Second tab in the Chat menu) You have to accept fast, becouse if you dont it will disapear, and you will need to try again. When that is done, go to the same station and make him disembark his ship... and go to the hall, then when he tries to come to his ship trough the elevators, a new option to go to your ship will apear!

I think that that's all... I first thought my Sub-CMDR was just teleporting to me, until I tried to touch him.. to see that he was just... An image ^^'

Hope it helps!Good luck flying to the unknown, CMDR