This happened for me after upgrading a site from DNN 5.4 to DNN 6.0.1. The menu on the site opened under or behind the modules on the page. The modules actually covered up the menu. I searched a long time online for the trick to get the menu on top again. James Godbold at DRNuke.co.uk sent me the solution. Since the links I found had little success fixing the problem, I want to publish James's solution now. Here it is:

"This is a bug in DNN overriding a skin style.

Go to Admin > Site Settings and scroll down to the stylesheet editor. Add the following CSS to the end of the stylesheet.

.MainMenu_SubMenu { z-index: 1000 !important; }

Click “save style sheet” and refresh the site."

Thanks James!