You can do that in PHP, I just don't know why you wouldn't use the JS anyway since its required to show the code.
$iDuration = 5;
$bShowIt = !isset($_COOKIE['lastShown']) || isset($_COOKIE['lastShown']) && (time() - $_COOKIE['lastShown']) > $iDuration ? true : false;
setcookie('lastShown', time(), time() + $iDuration);
// do whatever you gotta do to show it
printf('Show something every %d seconds', $iDuration);
Looks like it'd do the trick. Server languages tend to limit their reliance on cookies as much as they can.