Okay, so i'm going to run by everything i did, and maybe we'll figure out where the flag got messed up.
First day, i accepted the three quests (Find the boy, retrieve the mace, find the daughter) and got all three done at the same time. The boy helped drag Stella to the boat again after raising the drawbridge.
I then handed in the three quests, for the Prioress i picked "I did it for the troops" for the... +1 Intrigue i believe, then talked to her about the battle and the Abbey, turned in the other two quests and the next day i went in to save Sir Thomas, Mother and Marie via Tubbers.
On the ship, i again made a slight detour to talk to the Prioress again (she's taking care of the seasick villagers) and the quest never switched back to Failed for me.
Anything of the above list that you did differently?