I am also having this experience and it is quite annoying. I had updated Safari prior to Lion. After the Lion installation, the first time that I ran Software Update, it gave me the new version again. Currently on my system is version 5.1 (7534.48.3). I do not want several windows for places I'm not going back to opening. I do want it opening to the same page each and everytime. Like Jet787, I have the appropriate boxes checked but I did not try the reopen windows setting. Any help would be appreciated.