My wife is now using my Incredible since I upgraded to the Inc 2, but to try and answer your question. I rooted the same way with gingerbreak and have the same issues your having. As far as it going back to default, it's because we dont have custom recovery on our setup (someone correct me if I'm wrong here) there is one available to use
Here I just havent tried it out yet. I hope someone comes up with a ROm for this phone. I keep it just for a backup in case anything happens to my or her phone