Why this code not showing up on my site?

Have you tried removing the navigation mod code?

Still, you don't need two codes modifying the same thing

Sometimes the resize forum width code can conflict with codes. Could you temporarily remove that.

These are in your footer, but should be in your global header, at the top:

<script type="text/javascript">
//Move "Hey X, you have X" around welcome table
//wooper

var Position = "3"; //set the position. 1 is above everything, 2 is above menu, 3 is below menu
var pm = document.getElementsByTagName('TD')[2];

var hey = pm.getElementsByTagName("FONT")[0].innerHTML;

pm.style.display="none";

if(Position == "1")
{
var cell = document.getElementsByTagName("TABLE")[1].insertRow(0).insertCell(0);
}
if(Position == "2")
{
var cell = document.getElementsByTagName("TABLE")[1].insertRow(1).insertCell(0);
}
if(Position == "3")
{
var cell = document.getElementsByTagName("TABLE")[3].insertRow(1).insertCell(0);
}
cell.colSpan = "2";
cell.align= "center";
cell.height="50";
cell.className = "windowbg";
cell.innerHTML = hey;
</script>

<script type="text/javascript">
<!--
/*Remove <<Tags>> Welcome Table*/
document.getElementsByTagName('font').item(1).style.display="none";
//-->
</script>

Good. I see these in your footer. It's duplicated, but moreover, you need to remove it at emails must be opt in by the user:

<script type="text/javascript">
/* PM Prefs Selected "Yes" By Default By Son Of Exodia */
/* Main Footer - Repost ONLY With Header Intact. */
/* forum.duelistselite.com & support.proboards.com */

if(document.location.href.match(/pmprefs/i) && !document.cookie.match(/_prefs=1/i)){
document.getElementsByName("emailme")[0].selectedIndex="1";
document.getElementsByName("alert")[0].selectedIndex="1";
document.cookie="_prefs=1";
}
</script>


<script type="text/javascript">
/* PM Alert Selected "Yes" By Default on PM Pref Page By Son Of Exodia */
/* Main Footer - Repost ONLY With Header Intact. */
/* forum.duelistselite.com & support.proboards.com */

if(document.location.href.match(/pmprefs/i) && !document.cookie.match(/_prefs=1/i)){
document.getElementsByName("emailme")[0].selectedIndex="1";
document.getElementsByName("alert")[0].style.display="none";
document.cookie="_prefs=1";
}
</script>
[/size

then could you remove the category splitter for me, temporarily.

I can't see any reason why it isn't working, other then removing all other codes, and seeing it it works by itself, i can't really suggest anything else. You will need to contact subdevo, as it's his code, he will be best equipped to help you.

No worries, and good luck