Hi Sarah,

You can post your question in Joomla Forums about JA Fixel
http://www.joomlart.com/forums/forumdisplay.php?467-JA-Fixel

For more, JA Fixel top menu have designed to be a sticky menu.
It use its own function in the template itself rather than the default sticky menu function of T3.

You can try to remove a block of code in /templates/ja_fixel/js/script.js (line 754 - 776)

(function(){
// Add class for mainmenu when scroller
var light = null,
sid = null,
mainnav = $('#t3-mainnav');

if(mainnav.length){
$(window).scroll(function() {

if(light != $(window).scrollTop() > mainnav.outerHeight(true) * 1.5){
light = !light;

light ? mainnav.addClass('affix') : mainnav.removeClass('light-mainnav');

//force reflow
mainnav[0].offsetWidth;

light ? mainnav.addClass('light-mainnav') : mainnav.removeClass('affix');
}
})
}

})();

Hope it helps,

Regards