Well the permissions thing may have worked Swanhg but I had the same problem as you ie. " enter one address in the address bar, but once I click on a link within that first website I can no longer use the address bar to visit another site, and am forced to reopen Safari ".
My problem began right after I upgraded Java. I had a WD My Cloud app that would allow me to access my MyBookLive drive from anywhere outside my home. It required Java, which I thought was installed. Guess it wasn't because the app kept saying "plugin missing". I went to the Java site, downloaded and installed it because I wanted to test out the remote access of MyBookLive with a web browser. *
Right after that Safari didn't work properly, Opera didn't work properly, side swiping didn't work, the App Store didn't work properly including . But because I just got Java workiing I thought what the **** it has to be Java. I uninstalled Java, rebooted and so far so good.
I'll try installing Java again but in any case, crap like this should not be happening.....
btw, you have to shut EVERYTHING but Finder down to install Java because if you don't it installs but Safari keeps telling you it's not there. Anyhew....