Should enable giving gifts to companions in your ship by maybe clicking on your companion and right clicking the gift. It does not make sense that you can't. Right now, you have to be outside your ship to give the gifts. And after you give the gifts and gain enough affection points, you have to go back to your ship when your companions want to talk to you "in your ship".

I had the same issue. I used a different computer and tried it and it worked! try using a different pc.