Flexslider has a callback API where you can execute functions after various actions:https://github.com/woothemes/FlexSlider/wiki/FlexSlider-Properties

 

I would check out the after callback and possibly the start callback and call refresh from there. For example:

 

$('#secondSlider').flexslider({

  animation: "slide",

  directionNav: false,

  controlNav: false,

  start: function() {

    $.waypoints('refresh');

  }

});

 

$.waypoints('refresh');必须加