I fixed it, in the tooltip().Render() function line 7570 in the source.
I changed plotTop which I couldn't figure out where it was set probably is not based on the current axis.
here is the change... I'll make a comment in github
placedTooltipPoint = placeBox(
label.width,
label.height,
plotLeft,
//plotTop, comment this out and replace with below...
point.series.yAxis.top,
plotWidth,
plotHeight,
{x: x, y: y},
pick(options.distance, 12),
inverted
);
http://highcharts.com/jsbin/ojuweg/2/edit