New experimantal implementation for Highcharts 4.1 is available at http://jsfiddle.net/gh/get/jquery/1.7.2/highslide-software/highcharts.com/tree/master/samples/highcharts/studies/alignthresholds/.
This implementation looks a the threshold on the primary axis (the one first defined), and aligns the threshold of any following axis to that of the primary axis.V. Raguraman commented
Hi Highchart Support Team,
I am reporting Highstock.js have a multiple axis alignment bug. Please see the mail which I got it from support team.
Right now this feature is not implemented in the core and it seems that the plugin isn't fully working. If you want, you can report it as a bug or leave a comment here: https://highcharts.uservoice.com/forums/55896-general/suggestions/2554384-multiple-axis-alignment-control?page=1&per_page=20.
Also, please refer Jsfiddle : http://jsfiddle.net/o9y5c1at/ for this problem.V. Raguraman commented
We are using Highstock.js column chart with zooming and scrolling. when we scroll the chart, the Y-axis and other secondary axes scale value getting updated, Due to this, the 0-axes is not aligning with the secondary axes correctly. Do you have solution for this problem.
Jsfiddle : http://jsfiddle.net/o9y5c1at/