atmega328p GPIO with 3.3V regulator reads 2.5V at pin when High
It turned out to be a bad reflow. When I removed the part (a 28QFN), I saw pins had sunk in the solder but not wetted (stuck to the pins). I reflowed a new micro and made sure it was really hot and now my boards work. You can kind of see it in this photo, but the pin in the upper left corner on the left side.