The first thing I did was completely deburr and smooth the holes before replacing the factory rubber rim strip with Velox. Didn't help. Only worked for a few hundred miles. My original theory was that it was the factory rim strip that had clearly extruded into the nipple holes.
It seems it was a confluence of the 42mm tire diameter and the rim size. I suspect that that's because the tire/rim combination forces the tube into a pear shape.
A layer of high pressure mylar rim tape and then the Velox over the top of that cured the problem. About a 1,000 miles now with no additional problems. Velox by itself didn't work and the high pressure tape by itself extruded too. The combination has worked fine and no problems with interference on getting the bead to seat .