I had a tire that would go flat within 100 miles every time. I changed tubes, changed rim strips, carefully went over every mm of the rim and tire inside and out but still got flats. I always orient the tire to the valve and use a Sharpie metalic marker to indicte the direction of rotation on the tube. This helped me identify that the holes were occuring in just about the same location each time. I was about to toss the tire when someone suggested that I turn the tire completely inside out to inspect it. I did and when I did the cotton ball test I found a tiny bit of metal, like the tip of a pin, embedded in the rubber. With the tire right side out it had passed the cotton ball, eye ball and finger tip tests, but inside out the point just barely came above the surface. My theory is that with the compression on each wheel rotation the tip of the pin just touched the tube, eventually wearing a small hole. I was able to extract the offending bit and the tire lasted the rest of the season without another flat.
The point (no pun intended) is that the things that cause flats can be sneaky, so you have to be very diligent in seeking them out.