I found the solution.
I had to set the layout.Compact property to true.

Hi,
I'm using the NGraphDataSourceImporter (with its VertexImported and EdgeImported) events to create vertices and edges. I'm using the following layout:
Dim layout As NLayeredGraphLayout = New NLayeredGraphLayout()
layout.Direction = LayoutDirection.LeftToRight
layout.EdgeRouting = LayeredLayoutEdgeRouting.Orthogonal
layout.Compact = False
layout.StraightenLines = True
layout.NodeAlignment = RelativeAlignment.Center

Please see the attached screenshot. The problem is that the yellow "Permit Issuance" vertex is not in the same line as the white "Permit Application" vertex on the right. How can I set that the 1st white vertex is the center vertically of the diagram, so it means that the yellow vertex will be in the same line as the white vertex?

Thanks,
Sandor Nagy