I used to run into this problem regularly when I had the shop. If the cap is not seating down far enough to put the primer in the top of the cap in contact with the nipple it does not want to fire the first time its hit.
Solution : Put the thread end of the nipple into a hand drill or drill press after you pad it so you don't ruin the threads and take a flat fine cut file and lay it flat against the nipple taking down the whole side evenly as it turns. Be sure to try the cap every little bit as you do not want it so loose it falls off; it should squeeze on but go all the way to contact with the primer. Lee