It's difficult to test with what you've provided, but you could try adding a z-index value to your 'ul#cssmw ul.level-1 > li > a { ' css rule in your CSSMenuWriter/cssmw/menu.css:
ul#cssmw ul.level-1 > li > a {
background-color: #999999;
background-image: none;
;
some more styles here;
;
padding: 6px 10px 6px 5px;
width: 150px;
z-index:999;
}
That might do it.