This is my attempt to add a short transition animation (fade in and fade out) for when the indicators when they appear or disappear. CSS transitions should work in this way, however for some reason still unknown to me, this transition is not applied. I made a standalone example in jsFiddle using pseudo elements to make sure this code is correct: http://jsfiddle.net/arasbm/95mhM/2/
I also tried using animation but that introduce some strange interference with scrolling. Let me know if you have an idea how to do this.