What 125x125 box? I only see five 117x30 boxes.
I opted for a different type of code for the new boxes. I used the code that Project Wonderful suggested which they claimed would allow more people to see the ads even if they have Javascript off. That's the only difference I know of that might explain why you see one set but not the other. Here is the code.
<!-- Beginning of Project Wonderful ad code: -->
<!-- Ad box ID: 21920 -->
<script type="text/javascript">
<!--
var d=document;
d.projectwonderful_adbox_id = "21920";
d.projectwonderful_adbox_type = "4";
d.projectwonderful_foreground_color = "";
d.projectwonderful_background_color = "";
//-->
</script>
<script type="text/javascript" src="
http://www.projectwonderful.com/ad_display.js"></script>
<noscript><map name="admap21920" id="admap21920"><area href="
http://www.projectwonderful.com/out_nojs.php?r=0&c=0&id=21920&type=4" shape="rect" coords="0,0,125,125" title="" alt="" target="_blank" /><area href="
http://www.projectwonderful.com/out_nojs.php?r=1&c=0&id=21920&type=4" shape="rect" coords="0,130,125,255" title="" alt="" target="_blank" /><area href="
http://www.projectwonderful.com/out_nojs.php?r=2&c=0&id=21920&type=4" shape="rect" coords="0,260,125,385" title="" alt="" target="_blank" /></map>
<table cellpadding="0" border="0" cellspacing="0" width="125" bgcolor="#eeeeee"><tr><td><img src="
http://www.projectwonderful.com/nojs.php?id=21920&type=4" width="125" height="390" usemap="#admap21920" border="0" alt="" /></td></tr><tr><td bgcolor="#eeeeee" colspan="1"><center><a style="font-size:10px;color:#0000ff;text-decoration:none;line-height:1.2;font-weight:bold;font-family:Tahoma, verdana,arial,helvetica,sans-serif;text-transform: none;letter-spacing:normal;text-shadow:none;white-space:normal;word-spacing:normal;" href="
http://www.projectwonderful.com/advertisehere.php?id=21920&type=4" target="_blank">Project Wonderful - Your ad could be here, right now.</a></center></td></tr></table>
</noscript>
<!-- End of Project Wonderful ad code. -->