A: 

You problem is that the error template is shown in the adorner layer which in your case will be at the root window.

If you were to change your code to the following you wouldn't have a problem, because there would be a separate adorner layer created around the rest of you controls.

<Window x:Class="GunMiser.Views.Shell"
xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation"
xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
xmlns:cal="http://www.codeplex.com/CompositeWPF"
xmlns:controls="clr-namespace:GunMiser.Controls;assembly=GunMiser.Controls"
Title="Gun Miser"
Height="768" Width="1024">
<Canvas>        
    <AdornerDecorator>
        <Canvas>
            <ContentControl x:Name="FilterRegion" cal:RegionManager.RegionName="FilterRegion" Width="326" Height="656" Canvas.Top="32" VerticalAlignment="Top" HorizontalAlignment="Left" />
            <ContentControl Name="WorkspaceRegion" cal:RegionManager.RegionName="WorkspaceRegion" Width="678" Height="726" Canvas.Left="330" VerticalAlignment="Top" HorizontalAlignment="Left"/>
            <Button Click="GunsButton_Click" Width="75" Height="25" Content="Guns" Canvas.Top="3" Style="{DynamicResource GunMiserButtonStyle}"/>
            <Button Click="OpticsButton_Click" Width="75" Height="25" Content="Optics" Canvas.Left="81" Canvas.Top="3" Style="{DynamicResource GunMiserButtonStyle}"/>
            <Button Click="SettingsButton_Click" Width="56" Height="28" Content="Settings" Canvas.Left="944" Style="{DynamicResource GunMiserButtonStyle}" HorizontalAlignment="Left" VerticalAlignment="Top"/>
            <Button Click="AccessoriesButton_Click" Width="75" Height="25" Content="Accessories" Canvas.Left="239" Canvas.Top="3" Style="{DynamicResource GunMiserButtonStyle}"/>
            <Button Click="AmmunitionButton_Click" Width="75" Height="25" Content="Ammunition" Canvas.Left="160" Canvas.Top="3" Style="{DynamicResource GunMiserButtonStyle}"/>
        </Canvas>
    </AdornerDecorator>
    <controls:PendingChangesConfirmationDialog x:Name="PendingChangesConfirmationDialog" HorizontalAlignment="Stretch" Margin="0,0,0,0" VerticalAlignment="Stretch" Width="1008" Height="730" Visibility="Collapsed" Panel.ZIndex="100" />
</Canvas>

Caleb Vear
Thanks for the answer, I don't have the code available to try (I'm working off-site), but I'll comment when I get back to it (it might not be till August :)).
Kevin