Background
Flash objects are not layered within the HTML like other HTML elements; by default, flash objects will always be layered on top of all other elements.
The Problem
Because Flash objects are always layered above all other HTML elements, if they overlap with your submenu, the submenu will be partially obstructed. Unfortunately, Flash objects are not affected by z-index.
The Solution
The Flash object can be made to layer properly by adding the wmode parameter and setting it to opaque or transparent
Here’s an article on wmode.
Object tag
Within an object tag, add this parameter:
<param name="wmode" value="opaque">
Embed tag
To the embed tag, add the following attribute:
wmode="opaque"
YouTube video (iframe)
add ?wmode=transparent to the embedded link like this:
<iframe title="YouTube video player" width="480" height="390"
src="http://www.youtube.com/embed/lzQgAR_J1PI?wmode=transparent"
frameborder="0" wmode="opaque" >
(or, just use the newer HTML5 markup rather than the flash markup – but better cross browser compatibility)
If you do not have direct editing capability of your flash markup, you’ll need to ask the author of the theme/plugin how you can add or edit the wmode parameter.