It seems there is a lot of problems on size for nodes in FlowGraph control. 

First : 

When saving a node, some weird modifications will be done only on height. 

...

Why height and not width ? And i think, because UserSize is saved and not ActualSize, you don't have to do this (see below).

Second :

Take the flowgraph sample, select a node, resize it only on height, you will see that the width will be enlarge by 2 pixels.

Finally :

It seems that the function SetSize on a node enlarge all dimensions given by 2. In memory, we have UserSize + 2 = ActualSize. All calls on this method must be done with UserSize. When a node is serialized, the call to SetSize is made with UserSize but in the resize function (CXTPFlowGraphControl::StartResizeNode) is made with ActualSize.

L.

<Border xmlns='http://schemas.microsoft.com/winfx/2006/xaml/presentation' xmlns:x='http://schemas.microsoft.com/winfx/2006/xaml'

x:Name='nodeFrame' VerticalAlignment='Center' HorizontalAlignment='Center' Padding='0' BorderThickness='1' BorderBrush='#717171' >

   <StackPanel x:Name='nodeContent' VerticalAlignment='Center' HorizontalAlignment='Center' Background='#DCDCDC'>

      <Border x:Name='nodeCaptionBorder' BorderThickness='1' BorderBrush='#717171' Background='#ACACAC' Padding='20, 0, 20, 0' CanSetColor='True'>

         <WrapPanel>

            <Image x:Name='nodeImage' Margin='-20,0,0,0'/><TextBlock x:Name='nodeCaption' FontWeight='Bold' VerticalAlignment='Center' HorizontalAlignment='Center'/>

         </WrapPanel>

      </Border>

      <StackPanel x:Name='nodeCustomControl'/>

<StackPanel x:Name='nodeItemsCollection'/>

</StackPanel> <!-- nodeContent -->

</Border> <!-- nodeFrame -->