Well, you could insert a custom jQuery javascript to alternate colors on the <ul> of the menu...
You would just have to make your selectors be every nth child = a certain color. Let me see if I can make this happen quick and I'll post it.
*EDIT*
Yeah, so, this will work, as long as you use the correct class selectors for the menu you want to change:
Code:
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.3.2/jquery.min.js"></script>
<script type="text/javascript">
$(document).ready(function() {
$("li:eq(0)").css("color","blue");
$("li:eq(1)").css("color","black");
$("li:eq(2)").css("color","red");
});
</script>
The correct selector for the theme *should be* 'ul#rmenu2 li'...I think.