I had a similar issue when I had my 3 most recent balls drilled. My thumb was also moved up slightly and the pitch changed due to the fact that I was always tearing my thumb with the old span length (would tear at the base of the thumb and on occasion would tear the side due to the thumbhole shrinking.) Also, the pitch was too far forward on the old balls.
The solution was to bevel the thumb more, and it did the trick. I also added a thumb slug to all of the new balls, so this way the feel is consistant. It's nice to not rely on the Robby's skin protector like I used to.
My arsenal
Heavy Oil: Storm Virtual Gravity Nano: 4000 AB
Medium-Heavy Oil: Still to be determined
Medium Oil: Roto Grip Nomad Dagger: 1500 polished
Medium-Light Oil: Roto Grip Rising Star: 1500 polished