I got it to work. I moved my call to menu.php further down my page into the nav area.

BEFORE

<div id="logoWrapper">
<div id="logo"></div>
<div id="taglineWrapper">
<?php
if (HEADER_SALES_TEXT != '') {
?>
<div id="tagline"><?php echo HEADER_SALES_TEXT;?></div>
<?php
}
?>

<?php
if (SHOW_BANNERS_GROUP_SET2 != '' && $banner = zen_banner_exists('dynamic', SHOW_BANNERS_GROUP_SET2)) {
if ($banner->RecordCount() > 0) {
?>
<div id="bannerTwo" class="banners"><?php echo zen_display_banner('static', $banner);?></div>
<?php
}
}
?>

</div>

</div>
<?php include('http://www.madminis.com/menu.php'); ?>
<!--eof-branding display-->

<!--bof-navigation display-->
<div id="navMainWrapper">
<div id="navMain">
<ul class="back">
<li><?php echo '<a href="' . HTTP_SERVER . DIR_WS_CATALOG . '">'; ?>Store <?php echo HEADER_TITLE_CATALOG; ?></a></li>
<?php if ($_SESSION['customer_id']) { ?>
<li><a href="<?php echo zen_href_link(FILENAME_LOGOFF, '', 'SSL'); ?>"><?php echo HEADER_TITLE_LOGOFF; ?></a></li>
<li><a href="<?php echo zen_href_link(FILENAME_ACCOUNT, '', 'SSL'); ?>"><?php echo HEADER_TITLE_MY_ACCOUNT; ?></a></li>


NOW
<div id="logoWrapper">
<div id="logo"></div>
<div id="taglineWrapper">
<?php
if (HEADER_SALES_TEXT != '') {
?>
<div id="tagline"><?php echo HEADER_SALES_TEXT;?></div>
<?php
}
?>

<?php
if (SHOW_BANNERS_GROUP_SET2 != '' && $banner = zen_banner_exists('dynamic', SHOW_BANNERS_GROUP_SET2)) {
if ($banner->RecordCount() > 0) {
?>
<div id="bannerTwo" class="banners"><?php echo zen_display_banner('static', $banner);?></div>
<?php
}
}
?>

</div>

</div>

<!--eof-branding display-->

<!--bof-navigation display-->
<div id="navMainWrapper">
<div id="navMain">
<?php include('http://www.madminis.com/menu.php'); ?>
<ul class="back">
<li><?php echo '<a href="' . HTTP_SERVER . DIR_WS_CATALOG . '">'; ?>Store <?php echo HEADER_TITLE_CATALOG; ?></a></li>
<?php if ($_SESSION['customer_id']) { ?>
<li><a href="<?php echo zen_href_link(FILENAME_LOGOFF, '', 'SSL'); ?>"><?php echo HEADER_TITLE_LOGOFF; ?></a></li>
<li><a href="<?php echo zen_href_link(FILENAME_ACCOUNT, '', 'SSL'); ?>"><?php echo HEADER_TITLE_MY_ACCOUNT; ?></a></li>

Thanks to all that help as especially kuroi for making an easy to use template