Brianma65,
I have had somewhat similar problems with the RCBS priming tool. At times, after seating a primer, the seating rod doesn't drop back to its proper lower position but hangs up near the shell holder (rod is off-centre as your photo shows). The solution was to press the white (in this case) holder for the shellholder farther into position by pressing on the butt end of the white holder or if too far, by pressing back on the white holder by pressing inward on the primer tray. You are using the proper rod for the small primers (white holder). The larger one is too large to fit. Give this idea a try to see if you can centre the rod.