I'm using Moodle 2.3.2, and a customized version of the Nimble theme. You can see our website at:
http://ucdavisextension-onlinelearning.net/
As you can see, we're using the custom menu that comes with the theme to aid students in navigation. I've overidden the renderer that displays the menu so that the "Login" link reads "Logout" when the user is actually logged in to the site, so I'm not afraid of a little PHP programming.
It's that last link, the one to Customer Service, that's causing me grief. It's supposed to open in a popup window, but I can't for the life of me figure out how to make that happen. I've tried overiding the renderer and passing parameters to the moodle_url object, and I've tried adding "target=_new" to the menu in site->appearance->theme settings.
If anyone can help, I would be very grateful.