I had this problem, too, but am using the very awesome Entrepeneur (yes, that spelling is correct) theme by Ollie McCarthy. I tried changing the first line, but then the links didn’t line up and my menu broke. So I had to change the index in all layers so everything would line up.
Here is the code I now have. The lines of hidden code were the original code before I changed the z-index values:
/** Main Navigation **/
.menu-header ul {position:absolute; top:99px; left:-5px; font-size:12px; letter-spacing:0px;}
.menu-header ul li {position:relative; display:block; float:left; margin-right:3px;}
.menu-header ul li a {position:relative; z-index:999; padding:10px 10px 15px 10px; color:#dcecf8; opacity:0.8}
/** PREVIOUS CODE: .menu-header ul li a {position:relative; z-index:99999; padding:10px 10px 15px 10px; color:#dcecf8; opacity:0.8} **/
.menu-header ul li a span {}
.menu-header ul li span {opacity:0; display:block; background:url(images/dark_blue_nav_highlight.png) scroll transparent no-repeat; position:absolute; top:-15px; width:217px; height:60px; z-index:998; }
/** PREVIOUS CODE: .menu-header ul li span {opacity:0; display:block; background:url(images/dark_blue_nav_highlight.png) scroll transparent no-repeat; position:absolute; top:-15px; width:217px; height:60px; z-index:99998; }**/
.menu-header ul li ul { background:#82789a; display:none; position:absolute; width:143px; top:32px; text-align:center; padding:0px 1px 1px 1px; font-size:12px; z-index:9999; opacity:1; border-radius:3px; }
/** PREVIOUS CODE: .menu-header ul li ul { background:#82789a; display:none; position:absolute; width:143px; top:32px; text-align:center; padding:0px 1px 1px 1px; font-size:12px; z-index:9999999; opacity:1; border-radius:3px; }**/
.menu-header ul li ul li a {display:block; width:123px; float:left; background:#82789a; color:#82789a; padding:10px 10px; margin-top:1px;}
.menu-header ul li ul li ul {top:0px; left:139px;}
Thank you, simma 101! I was practically whimpering last night because this didn’t work and I wanted to use it so much. It was great to get up on a Saturday morning and find a solution!