About the mitt:
DD has two Nokona gloves, both were bought when she was in high school. She's a junior in college now, and thanks to Bretman - who recently completely rebuilt both of them - they are like brand new gloves! The Nokonas are known for being lightweight, something DD, as a pitcher, really likes. But they always were thin in the palm area. If you think about it, pitchers catch a TON of balls thrown back by the catcher. Bretman put a built-in pad in the palm of both of her gloves, and it completely eliminated the sting. They were "floppy" before, and Bret reshaped them like they were when new. As a matter of fact, she didn't even have to break them in again - they were game ready! The Nokona gloves/mitts are a great investment, and will last a lifetime.
Not knowing what brand/quality mitt you have, it's tough to tell what the problem is. But from experience, if Bretman can't fix it, or give you a good recommendation, it's probably not able to be fixed.
About the pain:
My wife & I both used to catch DD at lessons until she was about 16. Both our hands (mainly thumb area) ached after a session catching her. We asked our doctor about it, and he custom made what's called a "Thermoplast splint" that slipped over our hand/thumb, and fit inside the catcher's mitt. Doctor said it's NOT the impact so much, but rather the bending back of the thumb that causes long-term pain/discomfort. We found out that (at the time) OSU's catchers used the same device inside their catcher's mitt. The bonus for us was that it was covered under our medical insurance.