Soooo I decided to give this game another shot (after I've lost my game saves yet again...) and now it looks like there is a bug with the Stewart. When I reached the point at which I have the access to my ship, I can't click on Stewart. There is no dialogue tree involved, nothing pops. I can't ask her about anything and stuff (and if I recall correctly you were able to talk to here anytime you wanted after you go your ship).
Here is my game save file: