I was trying to add a new menu in and was experiencing problems and for once I don;t think its me
in the main.

The problem showed up as menus not appearing and then ending up with 2 at once (the old bus scenario

It seems to be down to publishing menu modules in the left area and this bit of code in index.php
countModules('right')) : ?>
Which I think says only display left and right modules if there are some right modules., so you end up only getting a left module displayed if a right module is also published.