Alan Jones, who used to develop primers for CCI backed up what the late Creighton Audette wrote in the early 90's, that you can get ignition delays and related phenomena with improperly seated primers.
You want to make some measurements to see if the priming is falling short. A depth mic with 4 mm diameter probe is best for determining the depth of your small primer pockets. The depth probe that sticks out of the end of the beam on your caliper may be used, but it is challenging to get consistent readings because it is hard to get the bottom of the caliper perfectly square to the case head unless you have
a depth adapter. (CDCOtools.com has one for $10, but their site won't let me link to it directly: Measuring Tools tab | Calipers and Attachments, last item.) Without it, it may take several attempts to find a believable reading, but it can be done. Once you have that reading, measure the height of several of the #41 primers. Subtract them from the depth of the primer pocket, then subtract another 0.003", and that will give you the correct depth below flush with the case head and into the primer pocket they should be when properly seated.
Short of all the measuring, you may also be able to fix this just by priming hard.
"There is some debate about how deeply primers should be seated. I don’t pretend to have all the answers about this, but I have experimented with seating primers to different depths and seeing what happens on the chronograph and target paper, and so far I’ve obtained my best results seating them hard, pushing them in past the point where the anvil can be felt hitting the bottom of the pocket. Doing this, I can almost always get velocity standard deviations of less than 10 feet per second, even with magnum cartridges and long-bodied standards on the ’06 case, and I haven’t been able to accomplish that seating primers to lesser depths."
Dan Hackett
Precision Shooting Reloading Guide, Precision Shooting Inc., Pub. (R.I.P.), Manchester, CT, 1995, p. 271.