I had the same problem with my Novack 3-white dot sights on my Kimber Pro Carry HD II. I tried the white paint - holes too deep, did not fill enough, turned yellow when I cleaned the gun. Tried the acrylic glow-in-the-dark paint - shrank too much, could not see them in daylight, needed time in the sun/under a lamp in order to charge, did not glow for very long. Tried self drying clay (craft store item, very white) - clay was too dry to manipulate and press into site holes, became off white as it was being worked. Finlay I tried this combo:3-dimentional fabric paint, since it shrinks I let it round over above the holes slightly. I then used a hobby knife to cut away the overflow but the plastic paint either pulled free of cut ragged. I Removed the paint and started over but this time I only put the paint in level with the rim of the holes. The paint shrank a bit but it was fine only it was shinny. To dull it down I used some flat clear paint and applied it with a tooth pic. When it dried I had flat white 3-white dot sights.
Later when that went bad I tried something desperate. I mixed 2 part epoxy with some enamel white paint and used that. It dries very glossy so I used the flat clear to dull it down. It has held up the best so far.