@Wolf With your hint I nailed it down to one of my panes in my Add-in. I have a webbrowser control inside my pane. If I remove it, the the white rectangle goes away. I'm using it so I can print html status messages to a console like window (my pane). Maybe ArcGIS doesn't support webbrowser control inside pane in this way? I'll have to think of an alternative way to display html if I can't fix.
<Grid>
<Grid.RowDefinitions>
<RowDefinition Height="*"/>
<RowDefinition Height="Auto"/>
</Grid.RowDefinitions>
<WebBrowser Grid.Row="0" x:Name="webConsole" Margin="10,5,10,0" ui:BrowserBehavior.Html="{Binding HtmlToDisplay}"/>
<ProgressBar Grid.Row="1" x:Name="ProgressBar" HorizontalAlignment="Left" Width="150" Height="10"
Margin="10, 5, 0, 5" IsIndeterminate="{Binding IsProgressIndeterminate}"
Visibility="{Binding IsProgressVisible, Converter={StaticResource BoolToVisibility}}"/>
</Grid>