Yep, her 3rd h-scene is accessed in a different way rather than just weapon upgrades. She should have 2 new options in her "talk" menu after her 2nd scene. After both of those the journal entry for Bunyan should update with a hint as to how to proceed in her quest.
If you'd like more specifics, there's a "hints" text file in the game folder that will have more details on how to get all the H-scenes.