Yes, placing your cheek against two different places on the stock will change the sight picture enough to cause different POI. I think you diagnosed your own problem.
There are lots of things PEOPLE can do to mess up groups, and when someone says they have been shooting percussiong rifles for a number of years, I tend to think(sometimes a wrong assumption) that the shooter must have put in the practice to be interested in shooting MLers that long, so he has fundamentals of hold, and head placement down well. I would not have thought about you putting your head on the stock in different places, unless I was actually watching you shoot.
When I sit down at a bench to shoot a gun for groups, I scuff my feet in the gravel, or dirt, or mark the cement some how so I know my feet are in the same place each time I sit down to take the next shot. I want to be in the same relative position to the gun stock, and have the barrel being held on the front rest the same way for each shot. Foot placement is just as important when shooting from a bench as it is shooting off-hand. I also use my hands to measure the distance from each side of the chair, or bench I sit on from the edge to each of my hips, again to make sure I am seated in the same place each time.
Oh, because guns differ, I have taken to using a technique I learned to use when testing lever action rifles, when I shoot all rifles. I move the forward rest back so that its right up against the front of the lever, or trigger guard, rather than balance the barrel or forestock way out towards the front sight. This causes me to sit up straighter, and I do have to raise the front rest up to allow me to use it this way. However, its better for breathing, seeing, and holding my sight picture without getting cramps in the muscles in my neck. Because most, if not all, of the barrel is forward of the front rest, the shots may hit lower, than when I shoot off-hand, but not so much that I will miss the target. By letting the stock " hang " off the barrel consistently for shot to shot, I am able to test the consistency of my loads, and not worry about fliers caused by irregular pressure put on the barrel and stock during the string of shots.
Be very consistent in how you load that ball down on the powder charge. Let the powder charge down the side of the barrel, by tipping the barrel to one side as you are pouring the powder into the muzzle. You don't want to compress the powder in a flintlock. Load the PRB slowly and stop when you feel the PRB " crunch " the powder. Mark your loading rod, and from that point on, load to the mark. Your goal is to keep the lead ball as round as possible without defects and being deformed by hammering it in the barrel with the rod, or leaning on the ball to seat it, as you may have done when shooting percussion rifles. Percussion rifels shoot the best groups when the powder is compressed, the opposite of the way to load a flinter for accuracy.
This last group you show us indicates that at the time you shot it, you had almost everything going correctly. I don't know how well you shoot a peep sight, the lighting conditions, the size of the peep compared to the front sight post, or bead, etc. There are a host of things that can make a group smaller or larger based on what you do. The kind of lube you use, as well as how much or how little you use makes a difference. The same goes for patch thickness, how you clean between shots, what you use to clean between shots, whether the powder has been sifted or not, what powder you use( brand and grade) etc.
