We've managed to fix this issue on our side. The fix will be available with our next minor release.
But you need to change your code. You should define the names for the panes and secondary axes created via constructor, as follows:
public XYDiagramPaneBase AddPane(string caption, bool isBigCaption)
// add a dummy series
chartMain.Series.Add(new Series("dummy", ViewType.Bar));
yaxis = Diagram.AxisY;
pane = Diagram.DefaultPane;
_isDefaultPaneInitialised = true;
yaxis = new SecondaryAxisY(caption);
pane = new XYDiagramPane(caption);
Diagram.SecondaryAxesY.Add(yaxis as SecondaryAxisY);
Diagram.Panes.Add(pane as XYDiagramPane);
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