I was on a trip with a person who got a dozen flats. He scrupulously checked the inside of the tire and the rim, and could find nothing that would puncture the inner tube. Ultimately he took the wheel to a bike shop and they discovered a small shaving in the wheel that was making the punctures. I assume this was created when drilling the holes for the spokes. We scratched our heads as to how it could puncture the inner tube, but afterwards he had no flats. You might want to take the wheel to a bike shop, or try to flush or blow out the rim on the assumption there is some loose shaving in there. Obviously there is something.