update repro

samples/ControlCatalog/Pages/CheckBoxPage.xaml.cs

@@ -7,6 +7,7 @@ namespace ControlCatalog.Pages
     public partial class CheckBoxPage : UserControl
     {
         private TextBlock myTb;
+        private int count;
 
         public CheckBoxPage()
         {
@@ -25,7 +26,7 @@ namespace ControlCatalog.Pages
         {
             base.OnPointerMoved(e);
 
-            myTb.Text = e.GetPosition(this).ToString();
+            myTb.Text = e.GetPosition(this).ToString() + ", " + count++;
         }
     }
 }

src/Avalonia.Themes.Fluent/Controls/PopupRoot.xaml

@@ -13,6 +13,7 @@
         <LayoutTransformControl LayoutTransform="{TemplateBinding Transform}">
           <Panel>
             <Border Name="PART_TransparencyFallback" IsHitTestVisible="False" />
+            <Border Background="Red">
             <VisualLayerManager IsPopup="True">
               <ContentPresenter Name="PART_ContentPresenter"
                                 Background="{TemplateBinding Background}"
@@ -20,6 +21,7 @@
                                 Content="{TemplateBinding Content}"
                                 Padding="{TemplateBinding Padding}" />
             </VisualLayerManager>
+              </Border>
           </Panel>
         </LayoutTransformControl>
       </ControlTemplate>