Holly, I think I know what you are describing. My gun hand thumb has a scar , the fingerprints are back , scar ran from top of thumb extending to the meaty part of hand. I cut some ligaments (I guess...I went thru a bunch of butterflies - no stitches as a kid) and for quite a while I had a heck of a time using that thumb.
Dull throbbing pain, and the thumb didn't want to cooperate.
I had a friend go thru this and Gary I believe is correct , hers was repetitive motion related, file cabinets of all things. A phyical therapist friend had her do some excercises and she is fine. Another thing she had to do was change how whe grasps some things , like using a mop, she does not wrap thumb around ,instead keeps alongside the handle. Little stuff like this.
Repetitive motion , injury /cut, or arthritis is what comes to mind...ligaments sounds like Gary assessed it.
Ask a PT friend about excersises and trying to determine original cause. Maybe you don't need to mop...will affect shooting.
Get well and heal up soon.