So I'm having the same problem with this as well. I continued on with the main scenario quests and didn't think anything of "A Recurring Problem" before since it was not seen as a main scenario quest.
Now when I talk to Minfilia, who is in Revenant's Toll, she has the "Good Intentions" quest but I cannot accept it until I unlock/complete all the hard mode trials.
I went ahead a redid the Ultima's Bane trial and returned to the Waking Sands but Minfilia is not there. I have no idea what to do and am afraid I may have to restart with an entirely new character since I can't continue on with anything otherwise :/