Our developers investigated this further and said that this behavior is expected since the SplitPane sizes and arranges the panes based on the ratio of the RelativeSize of each pane. The workaround here is to use different a different SplitPane for each ContentPane you want to use. Here is a simple XAML code snippet:
<igDock:XamDockManager >
<igDock:XamDockManager.Panes>
<igDock:SplitPane igDock:XamDockManager.InitialLocation="DockedTop" >
<igDock:ContentPane x:Name="centerDock" />
</igDock:SplitPane>
<igDock:SplitPane igDock:XamDockManager.InitialLocation="DockedTop" >
<igDock:ContentPane x:Name="bottomDock">
<Button Content="Data To Excel" Height="23" Name="ExportToExcel" Width="110" />
</igDock:ContentPane>
</igDock:SplitPane>
</igDock:XamDockManager.Panes>
</igDock:XamDockManager>