I've had problems with misfires on the range after cleaning. I did the same thing....run a few dry patches, pop a cap or two, run some more patches, and then load. What I'd find is that there would sometimes be residue that would build up in the nipple.....so now, prior to loading, I run a nipple pick through the nipple and give it a good shake with the nipple at the high end (so any crud might fall away from the channel.
Then, when I load, I tip the barrel so the channel is lower...this way some powder trickles into the channel, helping to ensure ignition.
That's
my story, and I'm sticking to it!
The other thing I've found is that there tends to be more of a problem with residue from caps on wet and/or extremely humid days.