Interesting thread.  After much research this seems to be a somewhat prevalent issue.  My twist is I am using the Mega Menu in DNN6.2.  I wanted to save time and use the html and style sheets provided with the installed skin with 6.2.  As it turned out the Action menu when deployed hid behind a banner image.  This was nicely solved by adding  ".DnnModule {z-index:1;position:relative;}" to my style sheet skin.css.

My second issue occurs due to an embedded pdf in an iframe.  The Mega Menu when deployed hides behind the pdf.  The research I've done suggests this to be an embedded object issue and not a z-index issue.  The Action Menu deploys properly over the pdf, but not the Mega Menu.

I attempted working with the z-index in a number of areas including the menu style sheet.  I've also attempted to add code to the Module Settings Advance Settings Footer Area.  The code created a div and another iframe after the module iframe.  Here is a copy of the source:

The iframe entries were added through the module.

Unfortunately, the transparency on the second iframe did not work; so this approach was abandoned.  The menu did deploy over the module with the embedded pdf, but because of the lack of transparency the pdf contents did not show through.

I'm wiritng because I am stymied.  The solutions presented in this thread did not work.

Regards,

Jack