Well the good news is that your CSS and JS appear to be loading correctly.
Thanks for actually providing reference links to look at!
The current html output looks like:
Code:
<ul id="flexmenu2" class="flexdropdownmenu">
</ul>
<ul id="flexmenu3" class="flexdropdownmenu">
</ul>
Your posted code uses an array named $pages_menu. I don't think this value is getting assigned to smarty by PHP. You can determine this by using webmaster mode and looking at the assigned variables. You could also wrap your added code in an if statement: {if $pages_menu} {/if} and see if the <ul> sections show up. Also remember that the orderby of the pages needs to be within the defined ranges.
I use this particular trick all the time, pretty cool that Phil does too.
I am pretty sure you are not getting the array set in PHP. Especially since you copied over the whole skin. All signs point to this. Check if it is set and get back to us.
-Mike