You're applying stacking: 'normal' to all series. When really, you only want to apply it to the 1st 2 series. Take stacking: 'normal' out of plotOptions and put it in the 1st 2 series:
$('#container').highcharts({
chart: {
type: 'column'
},
xAxis: {
categories: ['Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul', 'Aug', 'Sep', 'Oct', 'Nov', 'Dec']
},
yAxis: [{ // Primary yAxis
min: 0,
max: 400,
tickInterval:100
}, { // Secondary yAxis
min: -40,
max: 100,
tickInterval: 20,
opposite : true
}],
series: [{
yAxis : 0,
stacking: 'normal',
data: [29.9, 71.5, 106.4, 129.2, 144.0, 176.0, 135.6, 148.5, 216.4, 194.1, 95.6, 54.4]
}, {
yAxis : 0,
stacking: 'normal',
data: [144.0, 176.0, 135.6, 148.5, 216.4, 194.1, 95.6, 54.4, 29.9, 71.5, 106.4, 129.2]
}, {
yAxis : 1,
type : 'spline',
data: [35, 60, 77, 56.7, 34, 55, 66, 72, 90, 45, 56, 60]
} , {
yAxis : 1,
type : 'spline',
data: [24.3, 12, 41.2, 12.1, 4, 45, 31, 21.5, 9.3, 7.7, 13, 22]
}]
});