This code genereates 2 panes. In the second pane the zero line is missing. This alway occurs when there are positive and negative numbers in the series. A work around may be to define a Constant Line for value 0 with the same color + width as the zero line would have, but I would prefer a more elegant solution.
'Fill data with positive and negative numbers
Chart1.ClearData ClearDataFlag_AllData
Chart1.OpenData COD_Values, 2, 2
Chart1.Value(0, 0) = 50
Chart1.Value(0, 1) = -75
Chart1.Value(1, 0) = 75
Chart1.Value(1, 1) = -50
Chart1.CloseData COD_Values
'Set panes
Dim ax As Axis
Set ax = Chart1.Axis(YAxis_Main)
ax.Pane = 0
Chart1.Series(0).YAxis = YAxis_Main
Set ax = Chart1.Axis(3)
ax.YAxis = True
ax.Position = AxisPosition_Near
ax.Pane = 1
Chart1.Series(1).YAxis = 3
Chart1.RecalcScale
Chart1.Panes(0).Title.text = "First pane"
Chart1.Panes(1).Title.text = "Second pane"
ChartFx.zip