Now that you mention it, I remember some pain in my thumb as well; but, it was when I started to use the trackball, so a quite different issue. Then I got used to the new movements, pain went away in a week usage or so, and I was happy since then after.

Also, I remember being able to be more accurate with a trackball than I am now with a mouse, not having to worry about a mousepad, not needing space around the device other than that needed to rest your hand comfortably... Gosh, I can't find a reason why I went back to a mouse