I have never seen it necessary to paint a bullet for it to be "seen" by a chronograph. They generally work by detecting the shadow of the projectile against the bright background of the skyscreens. The color of the bullet shouldn't make any difference, but it obviously does in your case.
I may have been the one to start this off. My chronograph works fine with jacketed .30 cal rifle rounds, but had problems with slower .357 pistol bullets, particularly lead instead of jacketet/plated ones. I have no idea why, because as you say its the shadow that does the work of letting the sensor "read" as it passes. Someone years ago told me the trick of coloring with a felt marker & for some unknown reason it makes a big difference.
Something else that migh be having an effect, muzzle blast momentarily disturbing the plugs into the unit at the bench. I know it sounds odd, but I had a problem once with a rifle fitted with a "combination device" (muzzle break kind of thing). I suddenly got errors, which I'd not had before with un vented bores. The factory suggested moving the base unit & it fixed the problem. I guess the blast was "whipping" the cabling at close proximity, causing a brief continuity problem.
Allan Quatermain: “Automatic rifles. Who in God's name has automatic rifles”?
Elderly Hunter: “That's dashed unsporting. Probably Belgium.”