Try doing what Post # 142 here says....see if that works for you. I had the same issue since I rooted with Gingerbreak prior to the OTA updated. After that it said SuperUser still existed but nothing worked. After you run these commands run the OneClick root and see if that works for you:
Droid 3 root instructions (One Click added for Windows/ Linux/ OSX) - Page 15
Droid 3 root instructions (One Click added for Windows/ Linux/ OSX) - Page 15