Hello,
The Flex Menu hover color is echoed from your highlight color in the Template Manager. This coding in the index.php generates that hover color for the menu as well as other elements.
#s5_register:hover, #s5_login:hover, #s5_nav li .s5_level1_span1:hover, #s5_nav li.mainMenuParentBtnFocused .s5_level1_span1, a.readon:hover, a.pager:hover, button:hover, .button:hover, .pagenav a:hover, .s5_ls_readmore:hover, .readmore a:hover {
background:#<?php echo change_Color($s5_highlightcolor,'+35'); ?> !important;
}
So either change the highlight color or remove this part from the code:
#s5_nav li.mainMenuParentBtnFocused .s5_level1_span1