Bootstrap Carousel blocking position:fixed - wordpress

Question

I made a wordpress theme with bootstrap, it uses carousel and affix.
Now, when the carousel changes slide, the .affix isn't working over that period, when the carousel has finished the transition, the div with position:fixed is displayed correctly again.
You can check it here:
http://hu.rundertisch.org/?page_id=106
The navigation on the left side gets the position:fixed when you scroll to the bottom.
Just wait until the transition of the background image starts then scroll down. You see that the menu isn't moving with the screen. When the transition finished try again and you will see the difference.
I also have this problem with normal div's that have position:fixed like the wordpress top-admin bar that is displayed when you log-in. It just doesn't scroll witht he screen when a transition is going on.
This is my application.js that is included just before the (and wp_footer) tag, it is the last js file that I include after the whole bootstrap js files:
!function ($) {
$(function(){
var $window = $(window)
setTimeout(function () {
$('#af-me').affix({})
$('#ad-box-1').affix({offset: 580})
}, 100)
$('#running-box, #bg-car').carousel({})
$('#klapp').on('show', function () {
$("html, body").animate({ scrollTop: $(document).height() }, 365);
$('#col-switch').text("Becsukni");
})
$('#klapp').on('hide',function () {
$('#col-switch').text("Kinyitni");
})
$('a').click(function(){
$('html, body').animate({
scrollTop: $( $(this).attr('href') ).offset().top
}, 500);
return false;
});
$('#top').on('click',function () {
$("html, body").animate({ scrollTop: 0 }, 360);
})
$(".stop-car").hover(
function(){
$('#running-box, #bg-car').carousel('pause');
},
function() {
$('#running-box, #bg-car').carousel('cycle');
}
);
})
}(window.jQuery)