I found it myself!
As I said I am using Bootstrap menu, by default menu was opening on click events. Which I changed to hover event. But I didn't remove the jQuery which was hiding the current opened menu on document.click
event. This is the code I commented:
$(document).click(function() {
// Simply hide the submenu on any click. Again, this is just a hacked
// together menu/submenu structure to show the use of jQuery-menu-aim.
$(".popover_relation").css("display", "none");
$("a.maintainHover_relation").removeClass("maintainHover_relation");
});