I don't know how many rounds you have fired with the current nipple so I would first be looking at something else. Pull the nipple and inspect the barrel side of the nipple making sure tha it is clean and clear of any soot.
Next consider your cleaning procedures. Are you getting the chamber area clean and dry? Are you using and excessive amount of powder? Remember that every muzzle loader has its own likes and dislikes. It is possible that you are not getting a clean burn and when you load the next round you push everything left in the barrel down to the bottom and this will not ignite properly. Cleaning can and will do the same thing.
Check your patch for signs of how well your rifle is firing. You may need to change your lube to help soften the fowling or you are using too much lube and it is causing the chamber to get damp. This will cause mis-firing.
After a mis-fire, remove the nipple, drop a few grains of powder down the hole, replace the nipple and re-fire.
I shoot at least 5 - 10 rounds of skeet each weekend and I have used the same nipples for the past 3 years. I use RWS 1075 caps.
What ever you find, I hope you get it straighten out because mis-fires while at the bench can create a nice flinch.
Sincerely,
AJ