You're using PHP too, leverage that, use PHP to check your referrer, if its the same host have it drop a "1" into a var prevPage = ; in a script tag, if its not drop a 0, then just look for that 1 or 0 to determine visibility.
Personally though...
If I went to a site that fades in, I'd leave immediately. This isn't 1999 anymore, that kind of stuff is annoying and hinders user experience, its not a "bells and whistles" its just strictly annoying.
Now if you want to fade out the content pane while you ajax the new content when they click a link and fade in the new content when it comes back with ajax, that's fine, the time it takes to do that will probably be no greater than if they clicked to leave the page, but loading a blank site then fading it in, first thing I'd click is the back button and go someplace else.