I actually got rid of the borders too, for me i just looked for anything that said borders in the style.css sheet and changed it to
border: none;. So if you ctr-f borders and change all of them to
border: none; and test out to see if it goes away it should work eventually going down the style.css.
Also i had that problem with the twenty ten theme i updated wordpress to 3.0.2 and it deleted everything i did. so i started saving the theme folder every time i update so i can change it back. I need to figure out how to convert the theme to a child theme. That would be nice not having to worry about it disappearing. I was very upset when it happened.