.modal-open .dropdown-menu {
	z-index: 2050;
}
.modal-open .dropdown.open {
	*z-index: 2050;
}
.modal-open .popover {
	z-index: 2060;
}
.modal-open .tooltip {
	z-index: 2080;
}
.modal-backdrop {
	position: fixed;
	top: 0;
	right: 0;
	bottom: 0;
	left: 0;
	z-index: 1040;
	background-color: #000;
}
.modal-backdrop.fade {
	opacity: 0;
}
.modal-backdrop,
.modal-backdrop.fade.in {
	opacity: 0.8;
	filter: alpha(opacity=80);
}
div.modal {
	position: fixed;
	top: 50%;
	left: 50%;
	z-index: 1050;
	overflow: auto;
	width: 560px;
	margin: -250px 0 0 -280px;
	background-color: #fff;
	border: 1px solid #999;
	border: 1px solid rgba(0,0,0,0.3);
	*border: 1px solid #999;
	-webkit-border-radius: 6px;
	-moz-border-radius: 6px;
	border-radius: 6px;
	-webkit-box-shadow: 0 3px 7px rgba(0,0,0,0.3);
	-moz-box-shadow: 0 3px 7px rgba(0,0,0,0.3);
	box-shadow: 0 3px 7px rgba(0,0,0,0.3);
	-webkit-background-clip: padding-box;
	-moz-background-clip: padding-box;
	background-clip: padding-box;
}
div.modal.fade {
	-webkit-transition: opacity .3s linear, top .3s ease-out;
	-moz-transition: opacity .3s linear, top .3s ease-out;
	-o-transition: opacity .3s linear, top .3s ease-out;
	transition: opacity .3s linear, top .3s ease-out;
	top: -25%;
}
div.modal.fade.in {
	top: 50%;
}
.modal-header {
	padding: 9px 15px;
	border-bottom: 1px solid #eee;
}
.modal-header .close {
	margin-top: 2px;
}
.modal-header h3 {
	margin: 0;
	line-height: 30px;
}
.modal-body {
	overflow-y: auto;
	max-height: 400px;
	padding: 15px;
}
.modal-form {
	margin-bottom: 0;
}
.modal-footer {
	padding: 14px 15px 15px;
	margin-bottom: 0;
	text-align: right;
	background-color: #f5f5f5;
	border-top: 1px solid #ddd;
	-webkit-border-radius: 0 0 6px 6px;
	-moz-border-radius: 0 0 6px 6px;
	border-radius: 0 0 6px 6px;
	-webkit-box-shadow: inset 0 1px 0 #fff;
	-moz-box-shadow: inset 0 1px 0 #fff;
	box-shadow: inset 0 1px 0 #fff;
	*zoom: 1;
}
.modal-footer:before,
.modal-footer:after {
	display: table;
	content: "";
	line-height: 0;
}
.modal-footer:after {
	clear: both;
}
.modal-footer .btn + .btn {
	margin-left: 5px;
	margin-bottom: 0;
}
.modal-footer .btn-group .btn + .btn {
	margin-left: -1px;
}
And now the popup is display correctly.
The modal CSS added came from the default joomla 3 template.