Maybe it will help if I post all of my code:
As I mentioned this all was working perfectly until I updated to 2.0.
<Grid x:Name="MainGrid">
<ExtendedToolkit:WindowContainer Name="xWindowContainer">
<ExtendedToolkit:ChildWindow Name="ChildWindow" WindowState="{Binding ChildWindowVisible, Mode=TwoWay}" Caption="{Binding ChildWindowCaption}"
WindowStartupLocation="Center" IsModal="True" CloseButtonVisibility="{Binding ChildWindowCanExit, Converter={StaticResource BooleanToVisibilityConverter}}" Loaded="ChildWindow_Loaded"
SizeChanged="ChildWindow_SizeChanged" Closing="ChildWindow_Closing">
<ContentControl HorizontalAlignment="Stretch" VerticalAlignment="Stretch" Content="{Binding ChildContent}"/>
</ExtendedToolkit:ChildWindow>
<ExtendedToolkit:ChildWindow Name="ChildWindowError" WindowState="{Binding ErrorWindowVisible}" Caption="{Binding ErrorWindowCaption}"
WindowStartupLocation="Center" IsModal="True" CloseButtonVisibility="{Binding ErrorWindowCanExit}" SizeChanged="ChildWindowError_SizeChanged"
Loaded="ChildWindowError_Loaded" Closing="ChildWindowError_Closing">
<ContentControl HorizontalAlignment="Stretch" VerticalAlignment="Stretch" Content="{Binding ErrorContent}"/>
</ExtendedToolkit:ChildWindow>
</ExtendedToolkit:WindowContainer>
<Grid>
<Grid.RowDefinitions>
<RowDefinition Height="35"/>
<RowDefinition Height="*"/>
</Grid.RowDefinitions>
<Grid Grid.Row="0" HorizontalAlignment="Stretch">
<Border BorderBrush="Gray" BorderThickness="0,0,0,0.1">
<ContentControl Background="#FFF5F5F5">
<ToolBar Height="35" Background="Transparent" IsTabStop="False" ToolBarTray.IsLocked="True" Name="DionysusToolbar" HorizontalAlignment="Stretch" VerticalAlignment="Stretch"
Loaded="DionysusToolbar_Loaded">
<ToolBar.Items>
</ToolBar.Items>
</ToolBar>
</ContentControl>
</Border>
</Grid>
<Grid Grid.Row="1">
<DockPanel LastChildFill="True">
<odc:OutlookBar IsTabStop="False" NavigationPaneText="Expand navigationbar to view" DockPanel.Dock="Left" x:Name="OutlookBar" Width="300"
AllowDrop="False" HorizontalContentAlignment="Left" IsButtonSplitterVisible="False" IsCloseButtonVisible="False"
IsManipulationEnabled="False" IsMaximized="True" IsOverflowVisible="False" ShowButtons="True" ShowSideButtons="True" Loaded="OutlookBar_Loaded" VerticalContentAlignment="Stretch" />
<ContentControl Content="{Binding MainContent}" Grid.Column="1" Margin="0,0,2,0" Grid.Row="1"></ContentControl>
</DockPanel>
</Grid>
<Border Grid.Row="2" BorderThickness="0,0.1,0,0" BorderBrush="Gray">
<Grid Grid.Row="2">
</Grid>
</Border>
<ContentControl Grid.RowSpan="3" Grid.ColumnSpan="2" HorizontalAlignment="Stretch"
VerticalAlignment="Stretch"
HorizontalContentAlignment="Stretch"
VerticalContentAlignment="Stretch">
</ContentControl>
</Grid>
</Grid>
This way the window is shown behind my "MainContent" content control. If i do put the WindowContainer after the grid or topmost, I cannot access any of the other control.As I mentioned this all was working perfectly until I updated to 2.0.