The alpha channel values are lost when you put the icons into a .NET ImageList. Image.FromFile doesn't seem to work too. I have managed to load the icons with their alpha values preserved using the Icon class.

[code]
void m_CurrentDiagram_BoxCreated(object sender, BoxEventArgs e)
{
     if (m_CurrentDiagram.Boxes.Count % 2 == 0)
           e.Box.Image = new Icon(@"D:\FlowChartNET_ImageProblem\FlowChartNET_ImageProblem\script_opaque_48x48_XP.ico").ToBitmap();
     else
           e.Box.Image = new Icon(@"D:\FlowChartNET_ImageProblem\FlowChartNET_ImageProblem\script_48x48_XP.ico").ToBitmap();

     e.Box.Transparent = true;
}
[/code]

I guess loading the icons from a resource stream instead from files will work too.