My first thought is that your fit is off, putting too much weight on your arms and hands. Odd that it would only be around the thumb, unless the way you're holding the bars is doing it?
If you start changing the fit to address this, wait until a couple days after the pain goes away completely to ride. It's much easier to inflame something that's already hurting than when you're at 100% and you don't want to think you've got the wrong answer when you don't.