I replaced the original a while back and I noticed the newer one may be slightly larger in diameter than the original such that the caps don't seem to fit as well.
When it becomes mushroomed from use the cap will not seat all the way down. The first hammer fall only drives it down onto the nipple and the second hammer fall will fire the cap.
It sounds like this is definitely your problem. The slightly larger nipple acts the same as if it were mushroomed. I had the same problem many years ago, which is one reason I shoot flinters!
And, as Steve said, chuck the nipple in a drill and run it against a piece of sandpaper. Be sure to check it frequently with a cap to make sure you don't take too much off! Let us know how you do, inquiring minds need to know.
~Kees~