I have a php page that starts with a session_start() and it stores the user info in the session variables. After that it goes either into (1) the long loop script does calcula
It sounds like the problem isn't with the session in multiple windows, but with the first script running the long loop before outputting any headers, specifically the session ID cookie that other pages would need to use the same session. You should probably start the session and store your variables and then either redirect the user to another page for the long loop or output some kind of content, such as "Welcome! Starting Long Loop..."