It sounds like you simply have a broken implementation of intrasite user tracking. The usual logic is:

if ! tracking_cookie
    make new session ID
    log referer, browser, blah as initial data
    add entry page to track log for session ID
    send cookie with session ID when returning page
else
    add page to track log for session ID
[download]

Once you have set a cookie (with a session ID) reloading a page will still send that cookie to you provided the path is correct.