Checkbox Counter Resets as result of Conditional Logic plugin

I have a "Song Request" form that counts every checkbox selected from each genre. The value is added to the "# SONGS PICKED" element that is fixed at the bottom of the website. It worked flawlessly, until I added Ninja Forms Conditional Logic: http://ift.tt/2sKe0Uw

As you select a genre from the "Choose your songs from the genres below:" select field, the corresponding checklist appears, and the previous one (if one is selected) is removed from the HTML.

This causes the counter to start back at 1 when you select a checkbox from the current/new checkbox list. If you switch back to the previous genre, it picks back up where that list was counted up to.

Below is my jQuery:

jQuery(document).ready(function() {
    function updateCounter() {
        var len = $("input[type='checkbox']:checked").length;
        if (len > 0) {
            $(".counter").text('' + len + '');
        } else {
            $(".counter").text('0');
        }
    if (len == 1) {
            $(".multi").text('');
        } else {
            $(".multi").text('s');
        }
    }
    jQuery(document).on("change","input[type='checkbox']", function() {
        updateCounter();
    });
});

I really can't figure out how to lock in the value. Any help would be greatly appreciated, as this site is 99.99% finished and needs this fixed before I can launch. Thank you ahead of time!