@crapo,
Bounds of axis depends on multiple factors including the axis labels. In your case, ticks of axisY & axisY2 are not getting aligned as labels are shown for axisY, which takes up space towards the top of the axis & axisY2 doesn’t. You can overcome this either by reducing labelFontSize in axisY or by setting labelFontColor of axisY2 to be same as chart-background along with a negative margin. Please take a look at this updated JSFiddle for an example where ticks are aligning.
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Vishwas R
Team CanvasJS