I did two things that have almost completely eliminated that issue for me.I have been nettled by the same thing. I've even put some upgraded parts there to smooth things out, but it still happens on occasion. Often times, you get that spent primer hiding back near the drop tube, preventing new primers from seating all the way. Nothing's perfect I guess.
1. I created a little chute out of cardboard so that there is no gap between the primer drop and the cup. As you can see it's pretty high tech - I cut up a primer box and taped it in with aluminum duct tape.
2. I put a little metal magnet on the side of the primer chute door so that when the ram is raised, there's some additional weight to hold that closed so it won't prematurely drop a primer.