Bootstap Carousel won't work inside div

I'm building a website using Bootstrap and using Carousel at 100% height. The problem is that it works but not within another div. My Joomla system generates two div by default and so I can't avoid that. How should I resolve this issue?

HTML:

        <div>
        <div>
        <header id="myCarousel" class="carousel slide">
        <!-- Indicators -->
        <ol class="carousel-indicators">
            <li data-target="#myCarousel" data-slide-to="0" class="active"></li>
            <li data-target="#myCarousel" data-slide-to="1"></li>
            <li data-target="#myCarousel" data-slide-to="2"></li>
        </ol>

        <!-- Wrapper for Slides -->
        <div class="carousel-inner">
            <div class="item active">
                <!-- Set the first background image using inline CSS below. -->
                <div class="fill" style="background-image:url('http://placehold.it/1900x1080&text=Slide One');"></div>
                <div class="carousel-caption">
                    <h2>Caption 1</h2>
                </div>
            </div>
            <div class="item">
                <!-- Set the second background image using inline CSS below. -->
                <div class="fill" style="background-image:url('http://placehold.it/1900x1080&text=Slide Two');"></div>
                <div class="carousel-caption">
                    <h2>Caption 2</h2>
                </div>
            </div>
            <div class="item">
                <!-- Set the third background image using inline CSS below. -->
                <div class="fill" style="background-image:url('http://placehold.it/1900x1080&text=Slide Three');"></div>
                <div class="carousel-caption">
                    <h2>Caption 3</h2>
                </div>
            </div>
        </div>

        <!-- Controls -->
        <a class="left carousel-control" href="#myCarousel" data-slide="prev">
            <span class="icon-prev"></span>
        </a>
        <a class="right carousel-control" href="#myCarousel" data-slide="next">
            <span class="icon-next"></span>
        </a>

    </header>
    </div>
    </div>

CSS:

html,
body {
    height: 100%;
}

.carousel,
.item,
.active {
    height: 100%;
}

.carousel-inner {
    height: 100%;
}

/* Background images are set within the HTML using inline CSS, not here */

.fill {
    width: 100%;
    height: 100%;
    background-position: center;
    -webkit-background-size: cover;
    -moz-background-size: cover;
    background-size: cover;
    -o-background-size: cover;
}

JS:

$('.carousel').carousel({
    interval: 5000 //changes the speed
})

The code works if I remove the two "div" before and after <header>. How do I make it work? I cannot do away with the two div as it is generated by Joomla.