pickup point

I've known about this for roughly a year now, and I still cant figure out what variables are causing it. Ship B docks to Ship A ("mothership") via pickup point. Ship A fly's into another sector. Ship B vanishes at the boarder (and is left behind in the previous sector - in a "ghosted" state)...

I've been trying to get this to work for ages now, and i have a few solutions. (1) I tried to switch out the pickup point for a "Shootout Rail" but for some reason it wouldn't let me. Later i found out its button functionality was to turn it on and off.. not practical, i would prefer that...