Ситуация решилась добавлением в JCSmartFilter.prototype.hideFilterProps в else

$('div.active').removeClass('active');

.
Итог:

JCSmartFilter.prototype.hideFilterProps = function(element)
{
    var easing;
    var obj = element.parentNode;
    var filterBlock = BX.findChild(obj, {className:"bx_filter_block"}, true, false);
 
    if(BX.hasClass(obj, "active"))
    {
        easing = new BX.easing({
            duration : 300,
            start : { opacity: 1,  height: filterBlock.offsetHeight },
            finish : { opacity: 0, height:0 },
            transition : BX.easing.transitions.quart,
            step : function(state){
                filterBlock.style.opacity = state.opacity;
                filterBlock.style.height = state.height + "px";
            },
            complete : function() {
                filterBlock.setAttribute("style", "");
                BX.removeClass(obj, "active");
            }
        });
        easing.animate();
    }
    else
    {
        filterBlock.style.display = "block";
        filterBlock.style.opacity = 0;
        filterBlock.style.height = "auto";
 
        var obj_children_height = filterBlock.offsetHeight;
        filterBlock.style.height = 0;
 
        easing = new BX.easing({
            duration : 300,
            start : { opacity: 0,  height: 0 },
            finish : { opacity: 1, height: obj_children_height },
            transition : BX.easing.transitions.quart,
            step : function(state){
                filterBlock.style.opacity = state.opacity;
                filterBlock.style.height = state.height + "px";
            },
            complete : function() {
            }
        });
        easing.animate();
[B]$('div.active').removeClass('active');[/B]
        BX.addClass(obj, "active");
    }
};

Не знаю, насколько данный вариант верный, но вроде работает как надо :)