I have a problem with Highcharts where the Ceiling of one of my two y-axes is not being respected.
Y-axis \"1\" represents percentage values, so has a Floor of 0 and
I had a similar problem, but I found that using the following solves the issue:
maxPadding: 0,
minPadding: 0,
The default for these values are both 0.05 so that will be added to your data and cause highstock to make the y axis bigger than intended. Zeroing them out seems to fix the problem for me.
I also recommend to set the following so that maximum value still has a label:
showLastLabel: true,
http://jsfiddle.net/M4bVz/