One thing about muzzle loaders, you should wipe or clean the bore after each shot. You need to find a method that works for you. I have an old CVA and I have to wipe the bore after each shot to keep it accurate, if shooting for fun I do not. But I would use my rod and with one patch in and out just to keep the fowling down.
Lets think of it this way. Even with the new powers they tend to build up. Now this build up causes each shot to have a different pressure and then each shot will run down the bore different. Hence one shot here another there.
Then there is the primer itself, The 209 primer has a very hot flame and can cause a bit of fouling.
See this link.
Primers cause accuracy problems. It may help you understand what is going on. But the easy fix is to learn; wipe the bore after each shot. Use the same method to load powder, press the bullet in the bore, seat the bullet on the powder pellets, fire the gun, wipe the bore, start over doing the same steps, same motion, same pressure each time.
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