Did a quick search, didn't see anything that stood out (but this may be a duplicate). I don't have time to write a patch, but basically the following needs to be changed:

      // Handle select/unselect all
      $('#features-filter .features-checkall', context).click(function() {
        if ($(this).attr('checked')) {
          _checkAll(true);
          $(this).next().html(Drupal.t('Deselect all'));
        }
        else {
          _checkAll(false);
          $(this).next().html(Drupal.t('Select all'));
        }
        _resetTimeout();
      });

From:
if ($(this).attr('checked')) {

To:
if ($(this).is(':checked')) {