I had a similar problem when I returned to the sport after 10 years off.
I had my old ball fitted with a new slug that the driller drilled out egg shaped where the thumb hole was moved forward on the slug to accomodate my shorter pitch.
What resutled was thumb damage and callous on both sides of the thumb at the knuckle.
I have two choices now:
1) Take a while off and let the thumb shrink back to normal and have a slug fitted or:
2) Compress the callous' in every night I bowl by forcing the thumb in a smaller hole than the diameter of my thumb. The reason is that if I drill the hole to fit my thumb 'cold', it is then far too big when the callous/swelling compresses in.
I decided that since I'm addicted to bowling, I would have my thumb slug ovaled out on the sides and use Magic Carpets. Have had no problems since