Is it the same exact tire that flats? I don't know the answer to your problem, but last summer I started getting weekly flats in my rear tire. I found the location of the leak in the tube, carefully checked the tire for issues, and replaced the tube only to get another flat the next week. I even took the tire in to my LBS to see if they saw any problem. They didn't, so I again replaced the tube and the next week got a flat. I was running Schwalbe Marathon Plus tires, which should be pretty flat-resistant. Anyway, after five weeks of this, I threw out my rear tire, moved the Marathon Plus that was on the front to the rear, and haven't had a flat since. It's clear that my tire had some problem that neither I nor my LBS could detect. That's my experience, and when I was in your position, I discarded the tire that kept flatting, which solved the problem.