All of us have seen a Dotnetnuke website where the main menu of the site is hidden behind a module.  Recently we were contacted about this issue with our new module, Advanced News Ticker. 

A quick search revealed that this is something that can be fixed at the skin level.  I found the following thread on the Dotnetnuke Forum that explains how to fix the problem.

In particular interest this post:

You need to make sure you set the z-index in the css settings for the submenu items, for example, in skin.css you would have something like ".menuItemClass {z-index: 1000;}" to make sure the menu appears in front of input boxes, select drop downs, and flash.  The submenu really shouldn't need any z-index setting to simply have it appear in front of modules, unless you've got some erroneous setting in your css that is causing that to happen, like a position setting or display setting or even an incorrect or "not in proper order" z-index setting...  It can be tricky to set up.  Follow the menu setting and css files for the default skin, even do a copy paste into your skins files and then edit as necessary to match your design.