Possible bug: update_user_meta is updating two unique meta entries

Are you by chance using Firefox to test your page? If so its prefetching function combined with WordPress rel="next" could be the culprit. Check your page source for those rel tags, and see if Firebug registers an extra GET request to the page specified in the href attribute of the rel tag.

There is a Firefox extension Fasterfox, and it will prefetch everything. Disabling adjacent_posts_rel_link_wp_head will not help.
You should exit early in your code in those cases:

if ( isset ( $_SERVER["HTTP_X_MOZ"] ) and 'prefetch' === $_SERVER["HTTP_X_MOZ"] )
    return;