When the IsHidden property of a RadPane within a ToolWindow is set to True and then to false in quick succession, the ToolWindow is not shown. 

As a workaround, you can disable the animation of the ToolWindow:
<Style TargetType="telerik:ToolWindow">
<Setter Property="telerik:AnimationManager.IsAnimationEnabled" Value="False" />
</Style>

The above style need to be placed in the resources of the App.xaml in order to take effect on the ToolWindows, since they are displayed in a separated visual tree.