i slightly updated your demo at and have set transition time to 1000ms to easier recognise the animation. tooltip fade in and fade out - it works for me:

enter image description here

did not changed much, but removed the 'instant pop up' at mouseover:

      .on("mouseover", function(v) {
                  .duration(1000) //longer to easier be seen
                  .style("opacity", 0.9); //this is for the tooltip
              var text = "alert<br/>"+ formattime(v[0]) + "<br/>" + v[1];
                  .style("left", (d3.event.pagex)+"px")
                  .style("top", (d3.event.pagey-28) + "px")
                  .attr("fill", "steelblue");
                 // .style("opacity", 0.9); // not here

tested on latest desktop browsers as chrome 35, safari 7 and firefox 29. older opera 12 struggles with mouse over, maybe the tooltip overlays the point and therefore the mouse over does not count anymore. what browser do you use?

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