I can't ever seem to eat at the inn at night, even if I don't have any rations, but in can in the morning. Every morning after waking up, I get the "You don't have any food for the day" message before I even leave my room, but then I can eat downstairs and that seems to hold until the next day.
If I have rations, I must eat instead of getting that message, because I can't eat at the inn in the morning or evening, and my rations slowly deplete.