Session data lost in Chrome only
I had a very similar problem, in my case the problem was a 404 called due to a missing favicon.ico in Chrome only. The 404.php called the footer which altered the Session Variables.I hope that helps someone.
The issue could be your server is looking for favicons, if it is not found the server throws out a 302 redirect, which kills the session variables.
I had this issue and was able to fix it. Chrome keeps looking for a .ico file and for some reason it was affecting it. Once I placed the .ico file in the root of the site everything started working. Crazy but true.