Which one is Figure 1 and which one is Figure 2?
So when loading, do you reconstruct the GraphLinksModel in its entirety, and then you assign it to Diagram.Model? You don't do anything else after that assignment?
And then the link routes are wrong. I had assumed that the figure on the right is incorrect, but you did not make that clear. Then manually moving a node such as the one labeled "Module" causes all of the connected links to route correctly, yes?
Do you try to save and restore any link routes?
Do you have a minimal sample that reproduces this behavior so that I can debug it?