The reason they make VLD seating stems I would think is to prevent the tip of the bullet touching the end of the seating stem before it engages the ogive. Sounds like your new batch has a slightly different ogive....
"Anyone taking up handloading necessarily plays with unknown factors and takes chances. But so does anyone who drives a car,goes to a cocktail party,eats in a restaurant,or gets married."
Jack O'Connor 1963