I've adopted a policy of waiting until queens are mated and laying before marking. I figure that anything that makes her different, might interfere with the mating process and acceptance by the colony. Once they are laying well, I figure the colony will get healthy doses of pharimones, which might overpower any residual ink smells. I've marked early, and then found them quickly superseded. Last year I had one fly away while I was attempting to mark her.

Luckily she flew back to the parent hive and happened to enter above the queen exclude'r. I was happy to see her back, however she made a mess of my nice honey frames. 5 of my honey frames had become partial brood frames. I just moved her and those frames to another box, and voila, new hive. I'm using a queen marking kit to prevent a fly away in the future.