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Drag the chart around, eventually we will get the issue:
In short:
indexes are not updated after initial rendering in the redraw() function
current zIndex is miscalculated (uses top shape of the cuboid, while should use bottom one - it works with animation because.. height=1 so top shape and bottom shape are almost at the same place).
When animation is disabled, zIndex's are wrong, demo: http://jsfiddle.net/07ja16qg/
Workaround:
Instead of disabling animation, set the duration to 1: http://jsfiddle.net/07ja16qg/1/
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