You said you didn't find anything that would be causing flats inside the rim. I know it sounds kinda silly, but did you look with just your eyes or did you look with your fingertips as well? Many, many sharp spots that are invisible to the eye can be readily found by touch.
Just be careful you don't cut your hand. Another option is to get a soft, smooth piece of leather or cloth and run it over the tube-side of the rim. If you feel it catching, snagging, or getting tugged on anything, that'll give you some feedback. Do the same thing with the inside of the tire.

Having the last hole near the valve makes me suspect a metal bur or the like at the valve hole. Every time I've had repeated flats, there's been something (however small) that I've eventually found to cause them.

Good luck!