Melissa don't join you. Maybe you lost some relationship point to continue her story.
You gain 1 point rescuing her at the game start;
1+ when she join your party and then leave when you hit lv5(or when you go to the ruins mission);
1+when you help the priest clean the fountain;
1+talking to her at the forest;
1+training her in her room;
1+talking to her in front of the church.
If you did all of this, just keep doing your things, go back to the village after unlocking the F4 in the dungeon. You will have a event with Melissa at the village entrance.
Viewing post in Peasant Dream: Ascension comments
Her not being in her room is what confused me, she showed up again after Floor 4 with the Paladin quest, like you've said. So she'll just continue not be in her room until she comes back I guess, whenever that is.
It looks like I'm picking both girls, I wonder if there's a bad ending going down this path.