Did you set an AI personality for both main characters? If you are controlling a main character and start a dual dialogue, you will have to choose their answers even if they have an AI set.
Once you find the third star stone you will open up a room in the homestead containing a mirror you can use to re-do the cosmetic portion of character creation, including checking and changing the AI personality.
After AI personalities were first introduced a few people did report issues where it would stop working.
