Finally solved the issues. Upgraded to 7.2.5. After that the JD menus disappeared on the screen. Upgraded the JDMenu to 1.4.2 and same problem. Ended up the format and css of the menus had to be changed.

Here is the bad menu:
HTML

<_div id="menu_l">< <_div class="menu_r">< <_div class="menu">

CSS

#menu_l { height:59px; background:url(images/menu_l.png) no-repeat left top; position:relative; top:-5px; z-index:9999;}
#menu_l .menu_r { height:59px; background:url(images/menu_r.png) no-repeat right top;}
#menu_l .menu_r .menu { height:59px; background:url(images/menu_m.jpg) repeat-x left top; margin:0 47px 0 55px; }

Changed to this to make it work
HTML:

<_div id="menus">
<_div class="menu_l">
<_div class="menu_r">
<_div class="menu_m">
<_dnn:jdmenu runat="server" id="dnnJDMENU">
<_script type="text/javascript">

//
CSS:
#menus { top:-5px; z-index:10; position:relative; width:100%;}
.menu_l {height:59px; background:url(images/menu_l.png) no-repeat left top; }
.menu_r {height:59px; background:url(images/menu_r.png) no-repeat right top;}
.menu_m {height:59px; background:url(images/menu_m.jpg) repeat-x left top; margin:0 47px 0 55px; }