This hasn't been mentioned yet, but how long have you used a trackball? When I first got my Pearl, about a week or two later I noticed that my thumb was really sore, a little red, and it hurt to use the trackball. In my case my thumb was getting callused and after a while it didn't hurt anymore. Took a few weeks, but now I have no pain. Just a thought. Sorry if you really do have an allergy to it
Posted from my CrackBerry at wapforums.crackberry.com
If you are allergic to the material that the trackball is made of.. what about popping it out and coating it with a thin layer of clear nail polish or something? There's guides on the site that tell you how to remove it and put it back in correctly.
if you get scotch tape and put a thin layer on your thumb you won't come in direct contact with the track ball and you will get use the having the tape on pretty fast and people won't notice it
I also have a reaction to the trackball but I am not sure it is a rubber allergy. I have the same painful burning reaction when using my laptop scrollpad. Nickel maybe? I'm pretty bummed out because I just got my phone today.