Question

I could be wrong, but I think this might well be a bug of some kind:

http://jsfiddle.net/bRgUb/

               yAxis: {
                labels: {
                    formatter: function () {
                        return convertSecondsToHoursMinutesSeconds(this.value);
                    }
                },
                title: {
                    text: 'Time (h, min, s)'
                }

Answer 1

The Y axis is extended past the data range because of the default values for yAxis.minPadding and yAxis.startOnTick (see api.highcharts.com#yAxis).

Here’s your fiddle with those settings set to 0 and false: http://jsfiddle.net/highcharts/bRgUb/2/

            yAxis: {
                startOnTick: false,
                minPadding: 0
            },

I still recommend that you use type: “datetime” for the yAxis.