I ran into this on an alt character. It's an odd little quirk. As you probably already know, you need to get the quest from Minfilia, but she's obviously not giving it to you. As it turns out, since you didn't accept the quest before the point you are currently at, Minfilia now exists at two locations at once in the game. Try looking for her in the waking sands and you should be able to pick the quest up as if you hadn't pushed on with the main story quests.

Lore-wise, it's totally screwed up. I'm not sure why they made "A Recurring Problem" a required side-quest this late in the story rather than earlier.