Two things to check: 1. Do you bend the tip of your thumb back? 2. Where on your thumb do you place the rest?
Even though a bent thumb is a hard habit to break, keeping the tip of your thumb as straight as possible will reduce the strain. It will also make it easier to place the thumb rest further toward the hand (away from the end of the thumb). Even a small change can have a large effect on comfort. See it you can't get the thumb rest to sit on your knuckle, or just a little further out. It's awkward at first, but comes with practice.
These tips come from my own experience with pain, mind you.