Try this code. You don't need to check twice if the cookie is set since you're accounting for this at the top and setting to false. This code will set it to false if it is not set OR if (for some reason) it is not 'true'. Then, half way down, it will only need to check if it is true or not.
It's also best to just have a separate opening div open for each conditional, otherwise it can get very confusing and sloppy real fast.
<?php
if (!isset($_COOKIE['Seen']) || $_COOKIE['Seen'] != 'true') {
setcookie('Seen', 'false');
}
?>
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.9.0/jquery.min.js"> </script>
<script type="text/javascript" src="js/popup.js"> </script>
<LINK REL=StyleSheet HREF="style/style.css" TYPE="text/css" MEDIA=screen>
<html>
<head> </head>
<body>
<!-- Element to pop up -->
<?php
if ($_COOKIE['Seen'] == 'true') {echo '<div style="all:none; visibility:hidden; display:none">';}
else {
echo '<div id="element_to_pop_up">';
$value = 'true';
$expire = time()+60*60*24;
setcookie('Seen', $value, $expire);
}
?>
<a href="#"class="b-close" style="position:absolute; margin-top:5px; margin-left:550px;"><img src="./image/close.png"><a/>
<iframe frameBorder="0" name="iFrame" width="600" height="500" src="welcome.php" scrolling="no"></iframe>
</div>
</body>
</html>