We had this problem a lot during the beginning of the game, and it seems to be back now.
Sometimes when we have been in an instanced area, the portrait turns black and the dot on the minimap disappears whenever one of us gets outside the range of the other and when entering an instance, the other does not get a question of it wants to join or not. It only fixes itself if we leave the party and form it again every time it happens.
Also, when guesting someone story, not all the conversation windows the owner views shows up and sometimes, the cut scenes fail to trigger for the one guesting.
Edit: reforming the party does not seem to work anymore either.