checkbox function not working for dropdown menu

As per the wp_nav_menu() function the default classes are like below:

<ul class="menu">
    <li><a href="#">Menu</a></li>
    <li>
        <a href="#">Menu</a>
        <ul class="sub-menu">
            <li><a href="#">SubMenu</a></li>
            <li><a href="#">SubMenu</a></li>
        </ul>
    </li>
    <li><a href="#">Menu</a></li>
</ul>

Note that, the .menu and .sub-menu. May be you are messing with the wrong class names, and some class conflicts.