Is she taking any allergy medicine or using any allergy nosesprays like Astelin or Flonase? You can have a clear scope/CT and still have a lot of nasal tissue swelling which can cause the sinus headaches. The main source of the swelling is irritation from allergies.

I've been on shots for 3 years, but I still need to take the allergy meds and use the nosesprays. If your only experience with nosesprays is before surgery, then I would give them another chance. Before surgery, the spray probably didn't reach where it was needed.